Hi,
On Jul 23, 2015, at 2:51 PM, Robert Schmidt <[email protected]> wrote:
> Interesting Jack, thanks.
>
> Maybe you should put yours in easybuild.experimental?
>
> It seems like the underlying problem is that zlib is not included as a
> dependency of R (but is a dependency of libpng), thus the png tests fail due
> to missing symbols.
>
> Not sure if this is a EB bug or a package bug.
> It seems like something you would hope EB would deal with overall, but maybe
> there is something just a bit weird about this case and why the linker can't
> find the right version of zlib...
As far as I can tell it is a package bug. The pkg-config info for libpng is
incomplete and fails to list zlib as dependency for libpng. Pkg-config simply
cannot guess or smell it without the correct info in the libpng.pc file...
There is not much EB can do about it except for providing us with a machanism
to apply patches and capturing that in a recipe to reproduce the installation
on another site :).
The freetype2 bug is also a package bug. This one is "known", already fixed in
the freetype2 source and will be available in a future release:
https://github.com/s-u/Cairo/issues/13
https://savannah.nongnu.org/bugs/?45376
Cheers,
Pi
> On Thu, Jul 23, 2015 at 8:11 AM Jack Perdue <[email protected]> wrote:
> FWIW, if you are interested in R --with-x=yes, then
> see:
>
> http://www.siliconslick.com/easybuild/ebfiles_repo_cleaned/ada/R/R-3.2.0-intel-2015B-default-mt.eb
>
> and supporting packages:
>
> http://www.siliconslick.com/easybuild/ebfiles_repo_cleaned/ada/
>
> slick ( off to http://www.Quakecon.org )
>
> On 07/23/2015 06:37 AM, Pieter Neerincx wrote:
> > Hi Fotis,
> >
> > On Jul 23, 2015, at 4:20 AM, Fotis Georgatos <[email protected]> wrote:
> >
> >> Hi Pieter,
> >>
> >> On Jul 22, 2015, at 3:42 PM, Pieter Neerincx <[email protected]>
> >> wrote:
> >>> https://github.com/fgeorgatos/easybuild.experimental
> >>>
> >>> by creating an "issue" as per instructions in the README.md, but it looks
> >>> like Fotis Georgatos is on holiday... For now I forked the repo and
> >> No holidays here :) I’ve replied to that but it seems it went unnoticed:
> >> https://github.com/fgeorgatos/easybuild.experimental/issues/11
> > Aha, check I missed that.
> >
> >>> published the generator here:
> >>>
> >>>
> >>> https://github.com/pneerincx/easybuild.experimental/blob/master/users/pneerincx/generateEasyConfig.R
> >> No problem, just push your branch back to the original experimental repo;
> >> we do no PRs there at all, one less hop ;-)
> >>
> >>> DISCLAIMER 1: The generated easyconfig will contain any packages you had
> >>> installed and which are available from CRAN or BioConductor repo's.
> >>> If you have R packages from elsewhere you may have to tweak
> >>> the generator.
> >>>
> >>> DISCLAIMER 2: The generator assumes you will want an R with graphics
> >>> capabilities for plotting. Therefore it includes dependencies on
> >>> easyconfigs for various libs.
> >>> For libpng-1.6.17 and freetype-2.6 I had to create new
> >>> easyconfigs and patches as these libs contain bugs and some R packages
> >>> fail to compile with the plain vanilla libs.
> >>> I'll create a pull request for these new easyconfigs, but it
> >>> will take some time before these are available from the latest and
> >>> greatest EasyBuild release…
> >> Can you please share those in the experimental repo?
> >> Stefano was looking into this issue with png just last week.
> > I've added a README.md, some *.eb dependencies including libpng-1.6.17 and
> > freetype-2.6 and their patches. See:
> >
> >
> > https://github.com/pneerincx/easybuild.experimental/tree/master/users/pneerincx
> >
> > I'll push back to the original experimental repo in a few hours when I'm
> > back from a meeting....
> >
> > Cheers,
> >
> > Pi
> >
> >
> >> F.
> >>
> >> --
> >> echo "sysadmin know better bash than english" | sed s/min/mins/ \
> >> | sed 's/better bash/bash better/' # signal detected in a CERN forum
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> > -------------------------------------------------------------
> > phone: +31 6 143 66 783
> > e-mail: [email protected]
> > skype: pieter.online
> > -------------------------------------------------------------
> >
>
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phone: +31 6 143 66 783
e-mail: [email protected]
skype: pieter.online
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