Hi mailinglist,
I'm probably missing something here and unnecessarily complicating
things. I am trying to get R installed with just a few packages we
use. One of the packages, ggplot2, has a lot of dependencies. So when
I try to install R with one of the existing EasyBuild files and have
ggplot2 a
Howdy Niek,
FWIW, here is our latest build of R (with lots of
dependencies added):
http://www.siliconslick.com/easybuild/ebfiles_repo_cleaned/ada/R/R-3.2.0-intel-2015B-default-mt.eb
For extensions, we have another (non-EB) module (attached)
for installing extensions to the above by hand.
Betwe
Hi Jack,
Thank you for your answer. I don't understand the attached file. How
do you use that to install extensions, and how do you keep it so that
if you want to migrate to another cluster you can install R with the
exact same R libraries installed? Do you keep a separate file with all
the R pack
Hi Niel,
On 18/06/15 15:57, Niek de Klein wrote:
Hi mailinglist,
I'm probably missing something here and unnecessarily complicating
things. I am trying to get R installed with just a few packages we
use. One of the packages, ggplot2, has a lot of dependencies. So when
I try to install R with on
Howdy Niek,
We have a non-Easybuild module tree. The attachment
from before lives in /software/tamusc/modulefiles/R.
It loads the EB R and then sets the needed env vars
for building extensions.
Note that I don't maintain the R extensions so don't
have details. Here are the scripts written by m
Hi Niek,
I think many people in this list has suffer the R dependencies nightmare.
I wrote an small scirpt which if you already have a R easyconfig will try
to give you which are the latest versions available in R repos. It's not
perfect but it helps a little bit at least. Here you have it in cas
Thanks all!
On Thu, Jun 18, 2015 at 5:16 PM, Pablo Escobar Lopez
wrote:
> Hi Niek,
>
> I think many people in this list has suffer the R dependencies nightmare.
>
> I wrote an small scirpt which if you already have a R easyconfig will try to
> give you which are the latest versions available in R
Hallo Niek,
as Jack mentioned, we keep all our packages in a separate directory
and set the R_LIBS_USER env variable to that directory. For installing
there are actually 3 components
1) a module file
we have a different module (we name it R_tamu), the only thing it does
is to load the mat
Hi Maikel,
On 18/06/15 19:03, Marinus Pennings wrote:
Hallo Niek,
as Jack mentioned, we keep all our packages in a separate directory
and set the R_LIBS_USER env variable to that directory. For installing
there are actually 3 components
1) a module file
we have a different module (we nam
ubject: Re: [easybuild] Easier way of installing R packages
Date: Thu, 18 Jun 2015 19:48:11 +0200
From: Kenneth Hoste
Reply-To: easybuild@lists.ugent.be
To: easybuild@lists.ugent.be
Hi Maikel,
On 18/06/15 19:03, Marinus Pennings wrote:
Hallo Niek,
as Jack mentioned, we k
Hi Ken, all,
(Kenneth Hoste, Thu, Jun 18, 2015 at 04:32:27PM +0200:)
> We deliberately do not enable 'dependency=True', to ensure we can reproduce
> the exact same installation later; if you let R automagically resolve
> dependencies and let it pick the most recent version at that time for the
> d
Hi.
I had the same problem, and here how I solved.
I wrote this recursive function
https://github.com/stefanoberri/Rmisc/blob/master/retrievePkgNamesAndVersions.R
from an R installation where ggplot2 is installed you run
getPkgsTree("ggplot2")
this will return the list of package names and ve
Hi Riccardo,
On 19/06/15 10:32, Riccardo Murri wrote:
Hi Ken, all,
(Kenneth Hoste, Thu, Jun 18, 2015 at 04:32:27PM +0200:)
We deliberately do not enable 'dependency=True', to ensure we can reproduce
the exact same installation later; if you let R automagically resolve
dependencies and let it p
Hi,
On Jun 24, 2015, at 7:34 AM, Kenneth Hoste wrote:
> Hi Riccardo,
>
> On 19/06/15 10:32, Riccardo Murri wrote:
>> Hi Ken, all,
>>
>> (Kenneth Hoste, Thu, Jun 18, 2015 at 04:32:27PM +0200:)
>>> We deliberately do not enable 'dependency=True', to ensure we can reproduce
>>> the exact same ins
Hi Pieter,
On 24/06/15 10:58, Pieter Neerincx wrote:
Hi,
On Jun 24, 2015, at 7:34 AM, Kenneth Hoste wrote:
Hi Riccardo,
On 19/06/15 10:32, Riccardo Murri wrote:
Hi Ken, all,
(Kenneth Hoste, Thu, Jun 18, 2015 at 04:32:27PM +0200:)
We deliberately do not enable 'dependency=True', to ensure
Hi Kenneth,
On Jun 24, 2015, at 11:10 AM, Kenneth Hoste wrote:
> Hi Pieter,
>
> On 24/06/15 10:58, Pieter Neerincx wrote:
>> Hi,
>>
>> On Jun 24, 2015, at 7:34 AM, Kenneth Hoste wrote:
>>
>>> Hi Riccardo,
>>>
>>> On 19/06/15 10:32, Riccardo Murri wrote:
Hi Ken, all,
(Kenneth
> I would not know how to accomplish this without using R's own dependency
> handling mechanism and AFAIK their is no way to do this in Python.
Could this be done with rpy?
Niek
On Wed, Jun 24, 2015 at 12:53 PM, Pieter Neerincx
wrote:
> Hi Kenneth,
>
> On Jun 24, 2015, at 11:10 AM, Kenneth Hos
11:54
> To: easybuild@lists.ugent.be
> Subject: Re: [easybuild] Easier way of installing R packages
>
> Hi Kenneth,
>
> On Jun 24, 2015, at 11:10 AM, Kenneth Hoste
> wrote:
>
> > Hi Pieter,
> >
> > On 24/06/15 10:58, Pieter Neerincx wrote:
> >> Hi,
>
2015-06-24 10:58 GMT+02:00 Pieter Neerincx :
>
> Yesterday I started working on an R-script that generates an *.eb from an
> existing R installation. This is based on Stefano's code (Many thanks for
> sharing that!) and adds some commandline switches, help and code to figure
> out whether a packag
On Jun 29, 2015, at 3:37 PM, Pablo Escobar Lopez
wrote:
>
>
> 2015-06-24 10:58 GMT+02:00 Pieter Neerincx :
>
> Yesterday I started working on an R-script that generates an *.eb from an
> existing R installation. This is based on Stefano's code (Many thanks for
> sharing that!) and adds som
ok, thanks for your effort Pieter
2015-06-29 16:25 GMT+02:00 Pieter Neerincx :
>
> On Jun 29, 2015, at 3:37 PM, Pablo Escobar Lopez <
> pablo.escobarlo...@unibas.ch> wrote:
>
> >
> >
> > 2015-06-24 10:58 GMT+02:00 Pieter Neerincx :
> >
> > Yesterday I started working on an R-script that generates
Hi all,
It took a little longer, but I think I now have a fully functional
generateEasyConfig.R script that is ready for distribution; "It works on our
clusters" :)... I've requested access to
https://github.com/fgeorgatos/easybuild.experimental
by creating an "issue" as per in
Thanks for this. I just opened the 3.2.1-goolf-1.7.20 easyconfig PR. I'll
see if we should update any extensions.
Did you see the new Bioconductor Bundle (to separate it from the core?)
On Wed, Jul 22, 2015 at 10:43 AM Pieter Neerincx
wrote:
> Hi all,
>
> It took a little longer, but I think I
Hi Pieter,
On Jul 22, 2015, at 3:42 PM, Pieter Neerincx 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
Hi Pieter,
thanks for this work. I'll try it later.
> 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
Hi Stefano,
On Jul 23, 2015, at 11:58 AM, "Berri, Stefano" wrote:
> Hi Pieter,
>
> thanks for this work. I'll try it later.
>
>> 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 v
It does seem like x11 support is the key to getting the PNG capability. I
was working on it a bit yesterday and hope to figure it out today.
We need it for plot generation.
On Thu, Jul 23, 2015, 6:46 AM Pieter Neerincx
wrote:
> Hi Stefano,
>
> On Jul 23, 2015, at 11:58 AM, "Berri, Stefano"
> w
Hi Robert,
AFAIK you don't need X11 for PNG support, but I can imagine enabling X11 also
enables some dependencies some of which may also be required for PNG support
Cheers,
Pi
On Jul 23, 2015, at 12:54 PM, Robert Schmidt wrote:
> It does seem like x11 support is the key to getting the P
Hi Pieter,
Thanks a lot for the explanation.
I will try some workarounds while there is a fix for the libpng.
What you say makes sense. The issue arise when I try to install packages. At a
certain point the installation of a package complains about libz not being
available. I guess that libpng
Hi Fotis,
On Jul 23, 2015, at 4:20 AM, Fotis Georgatos wrote:
>
> Hi Pieter,
>
> On Jul 22, 2015, at 3:42 PM, Pieter Neerincx
> wrote:
>> https://github.com/fgeorgatos/easybuild.experimental
>>
>> by creating an "issue" as per instructions in the README.md, but it looks
>> like Fotis
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
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. I
Hi,
On Jul 23, 2015, at 2:51 PM, Robert Schmidt 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 du
Hi Fotis,
On Jul 23, 2015, at 4:20 AM, Fotis Georgatos wrote:
>
> Hi Pieter,
>
> On Jul 22, 2015, at 3:42 PM, Pieter Neerincx
> wrote:
>> https://github.com/fgeorgatos/easybuild.experimental
>>
>> by creating an "issue" as per instructions in the README.md, but it looks
>> like Fotis
Hi Pieter, all,
On Jul 23, 2015, at 5:18 PM, Pieter Neerincx wrote:
> pneerincx@yac8 ~/git/easybuild.experimental> git remote -v
> blessed https://github.com/fgeorgatos/easybuild.experimental.git (fetch)
> blessed https://github.com/fgeorgatos/easybuild.experimental.git (push)
“bless
I think I'm interested too. I'll ping you tomorrow.
On Thu, Jul 23, 2015, 10:09 PM Fotis Georgatos wrote:
> Hi Pieter, all,
>
> On Jul 23, 2015, at 5:18 PM, Pieter Neerincx
> wrote:
> > pneerincx@yac8 ~/git/easybuild.experimental> git remote -v
> > blessed https://github.com/fgeorgatos/ea
Hi Fotis,
On Jul 24, 2015, at 4:14 AM, Robert Schmidt wrote:
> I think I'm interested too. I'll ping you tomorrow.
>
>
> On Thu, Jul 23, 2015, 10:09 PM Fotis Georgatos wrote:
> Hi Pieter, all,
>
> On Jul 23, 2015, at 5:18 PM, Pieter Neerincx
> wrote:
> > pneerincx@yac8 ~/git/easybuild.expe
Hi Robert,
On Jul 22, 2015, at 4:47 PM, Robert Schmidt wrote:
> Thanks for this. I just opened the 3.2.1-goolf-1.7.20 easyconfig PR. I'll see
> if we should update any extensions.
Check, thanks! I just updated the generator to include 'LibTIFF', '4.0.3' (was
previously using a version provide
On Fri, Jul 24, 2015 at 8:35 AM Pieter Neerincx
wrote:
> No I completely missed that :o. Is this the "Standard Operating Procedure"
> the community has standardised on? If yes, I'd be happy to modify the
> generateEasyConfig.R to create to *.eb files - on for core and another for
> BioConductor.
Hi Pieter,
>> 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.
Can you show your output, within R, of capabilities(), along with the output of
lsb_release -a ?
A bug
Hi Fotis,
On Jul 25, 2015, at 11:32 AM, Fotis Georgatos wrote:
>
> Hi Pieter,
>
>>> 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.
>
> Can you show your output
s, I'll pick up from here when I am back
cheers
Stefano
> -Original Message-
> From: Pieter Neerincx [mailto:pieter.neeri...@gmail.com]
> Sent: 25 July 2015 16:25
> To: easybuild@lists.ugent.be
> Cc: Berri, Stefano
> Subject: Re: [easybuild] Easier way of installing
Hello,
This is a good moment to ask all others (who rely upon libpng as a dep for R)
to report,
if they have the png capability TRUE - if so, kindly supply your easyconfig,
somewhere!
On Jul 28, 2015, at 10:24 AM, Berri, Stefano wrote:
> I now have these "capabilities" in R-3.2.1
>
>> capabi
Hi,
> capabilities()
jpeg pngtiff tcltk X11aqua
TRUETRUETRUETRUE FALSE FALSE
http/ftp sockets libxmlfifo cledit iconv
TRUETRUETRUETRUETRUE
Hi,
On Jul 29, 2015, at 7:47 AM, Fotis Georgatos wrote:
>
> Hello,
>
> This is a good moment to ask all others (who rely upon libpng as a dep for R)
> to report,
> if they have the png capability TRUE - if so, kindly supply your easyconfig,
> somewhere!
>
> On Jul 28, 2015, at 10:24 AM, Ber
I have PNG capability now, but I needed to add libz as a dependency to the
R easyconfig. I also changed it to with-x
On Wed, Jul 29, 2015 at 1:47 AM Fotis Georgatos wrote:
>
> Hello,
>
> This is a good moment to ask all others (who rely upon libpng as a dep for
> R) to report,
> if they have the
Hi Pieter,
On Jul 29, 2015, at 1:45 PM, Pieter Neerincx wrote:
> Interesting indeed. Stefano, can you provide a list of R packages that fail
> to compile with freetype-2.6-goolf-1.7.20.eb + freetype-2.6.patch? It would
> like to see if I can reproduce that here...
Stefano will be off for a co
Hi Robert, Martin,
good thread this one.
On Jul 29, 2015, at 1:49 PM, Robert Schmidt wrote:
> I have PNG capability now, but I needed to add libz as a dependency to the R
> easyconfig. I also changed it to with-x
OK, zlib apparently was the missing piece, a very interesting build example
cam
On Thu, Jul 30, 2015 at 1:23 AM Fotis Georgatos wrote:
> I would lobby for a R/3.2.2 build (release to come out mid August),
> incorporating as much collective wisdom as possible, perhaps tuned for bio
> needs.
> What would you think? A PR upon 3.2.1 could be a first approximation of it.
I sett
Oh one more detail I try to keep the version of R, Rlib and Rprofile in
sync so that there's always a set of say "3.2.0", "3.2.1". I'll see how
that works out.
/Martin
On Thu, Jul 30, 2015 at 10:47 AM Martin wrote:
> On Thu, Jul 30, 2015 at 1:23 AM Fotis Georgatos
> wrote:
>
>> I would lobby
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