Summaries of my discoveries and solutions:
I now have these "capabilities" in R-3.2.1
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE FALSE TRUE TRUE TRUE TRUE
I build with
configopts = "--with-lapack --with-cairo --with-libpng --with-blas --with-pic
--enable-threads --with-x --enable-R-shlib"
but as I am connecting with putty, it shows X11 FALSE
NOTES:
I still could not fix the libpng issue properly. To solve it, I removed
dependency on libpng (rely on the system libs, I guess) but added
('zlib', '1.2.8') or installing some packages would have failed.
Also, since R-3.2.x, if I tried install.packages() I got an error saying
"internet routines cannot be loaded". I solved it adding dependency to
('cURL', '7.43.0'),
note that I now have libcurl capabilities. I found curl to be a constant source
of pain with R. Hopefully we should be sorted now.
Interestingly, previous versions of R (i.e. R-3.1.2) did not have any issues
with whatever cURL we had. Maybe we should explicitly set dependencies on cURL.
I am a bit puzzled that you have capabilites("png") = FALSE but are still able
to create png.
I guess we still need to understand the issue with libpng so that we can
properly point to a specific version and have easybuild to take care of it.
I hope this is somehow useful
I will be away for two weeks, I'll pick up from here when I am back
cheers
Stefano
> -----Original Message-----
> From: Pieter Neerincx [mailto:[email protected]]
> Sent: 25 July 2015 16:25
> To: [email protected]
> Cc: Berri, Stefano
> Subject: Re: [easybuild] Easier way of installing R packages
>
> Hi Fotis,
>
> On Jul 25, 2015, at 11:32 AM, Fotis Georgatos <[email protected]> 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, within R, of capabilities(),
>
> R> capabilities()
> jpeg png tiff tcltk X11 aqua
> TRUE FALSE TRUE TRUE FALSE FALSE
> http/ftp sockets libxml fifo cledit iconv
> TRUE TRUE TRUE TRUE TRUE TRUE
> NLS profmem cairo ICU long.double libcurl
> TRUE FALSE TRUE TRUE TRUE FALSE
>
> > along with the output of lsb_release -a ?
>
> $> lsb_release -a
> -bash: lsb_release: command not found
>
> But I guess this is more or less what you were looking for:
>
> $> cat /etc/redhat-release
> Scientific Linux release 6.6 (Carbon)
>
> > A bug on Stefano's side still persists and we need to understand some
> cause-effect chains...
> > ...namely, the png capability should be expected to be at TRUE value,
> correct?
>
> It's ... complicated. AFAIK there are many ways to create PNG images with R.
> In order to get png = TRUE from capabilities() you need X11, which is missing
> on many "headless" cluster nodes. In order to create PNG images without a
> dependency on X11 you can use Cairo Graphics. There are (at least?) two R
> packages to create PNGs with Cairo: Cairo and cairoDevice. I'm using Cairo
> which happily creates PNGs with png = FALSE from capabilities().
>
> See also http://r.789695.n4.nabble.com/How-to-get-R-to-compile-with-
> PNG-support-td3457938.html
> and https://gist.github.com/wch/2096726
>
> Cheers,
>
> Pi
>
> > tia,
> > Fotis
> >
> >
> > --
> > 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
> -------------------------------------------------------------
