[Rd] new bugs and new bundles Re: R/Sweave/cairo/freetype bug fix.

2013-09-03 Thread Hin-Tak Leung
The most up-to-date version of freetype (2.5.0.1) have problems with at least 
two of the system fonts shipped with Mac OS X. So the "p1" in "2.5.0.1p1":


cairo-1.12.16+freetype-2.5.0.1p1_macosx.tar.bz2
cairo-1.12.16+freetype-2.5.0.1p1_windows.tar.bz2

means "2.5.0.1" + 274207eb9a0e3bb20edf30e9a62e25120d5d15e5 (the fix for one of 
the problems). There might be p2 bundles if 2.5.1 doesn't come out soon enough

with fixes for the rest of the problems.

http://sourceforge.net/projects/outmodedbonsai/files/R/

Just so we are clear, if freetype have problem with a system font, fontconfig 
has problem with a system font, and cairo and R etc.


Unix users should just upgrade. I'll get round to build R 2.15.3 (or 2.15.x) for 
windows and Mac OS X at some stage, but if somebody want to beat me to it, 
please feel free to do so.


Hin-Tak Leung wrote:

Freetype 2.4.12 was released in early May. Just so that we are clear that this 
is a freetype bug which affects R's use of Cairo (among other things). So there 
are updated bundles, and also bundles for Mac OS X as well, for both a patched 
2.4.11 and 2.4.12 proper. The accompanying *.txt has a listing of versions.

http://sourceforge.net/projects/outmodedbonsai/files/R/

Unix users should just upgrade. I'll get round to build R 2.15.3 (or 2.15.x) 
for windows and Mac OS X at some stage, but if somebody want to beat me to it, 
please feel free to do so.

--- On Tue, 2/4/13, Hin-Tak Leung  wrote:


--- On Mon, 1/4/13, Hin-Tak Leung

wrote:

--- On Sat, 30/3/13, Hin-Tak Leung

wrote:


"... was committed to freetype in January and will

form

the

next release (2.4.12)".


It is perhaps worth repeating the quote:  'The

official

R binaries for windows ... are compiled against static
libraries of cairo 1.10.2 ... are firmly in the "do not

work

correctly" category'

The minimum version of cairo to work being 1.11.2. On

closer

examination, the official bundle 
(http://www.rforge.net/Cairo/files/cairo-current-win.tar.gz)
is built with neither fontconfig nor freetype. So even

if it

is bumped to current version (1.12.x), it does not

work

correctly.


Here is a drop-in replacement for the above:
http://sourceforge.net/projects/outmodedbonsai/files/R/cairo-1.12.14%2Bft%2Bfc-win.tar.gz

Besides being over 2 years more up-to-date, cairo (1.12.14)
is also built with fontconfig and freetype enabled, and
freetype being 2.4.11 + back-ported patch 
(https://bugzilla.redhat.com/show_bug.cgi?id=891457#c35)
so at least there is a a better chance of R working
correctly.

The full list of the tar ball is (a superset of the above,
due to addition of fontconfig and freetype and their
dependencies):
---
cairo-1.12.14
pixman-0.26.2
libpng-1.5.13
zlib-1.2.7
fontconfig-2.10.1
freetype-2.4.11 (patched)
glib2-2.34.3
expat-2.1.0
bzip2-1.0.6
libffi-3.0.11
gettext-0.18.2
-
This allows the C-based cairo bug demo (#c10) to build so I
am sure it is sufficient for building windows R. At some
stage I'll rebuild a less-buggy R 2.15.3 for windows, but
not for a few weeks so if somebody wants to beat me to it,
please feel free to do so.


Perhaps also wasn't clear in the bugzilla thread -

everybody

from fontconfig/cairo/freetype involved knew it being

the

issue so it has never been explicitly spelled out -

the

problem was (is) with cairo's pdf/ps generation, aided

by

freetype.


--
On Sat, Mar 30, 2013 18:54 GMT Simon Urbanek

wrote:



On Mar 30, 2013, at 9:24 AM, Hin-Tak Leung

wrote:



Perhaps that's too much details. There

is

(will be)

a new freetype because of cairo's unanticipated

usage

(which

R uses, among other cairo users). Most people

should

upgrade

or request an upgrade eventually, when they are
comfortable.




Which versions are affected? R binary for OS

X

uses

freetype 2.4.11 (and cairo 1.12.14) so I just need

to

know

if there is an action item.


Thanks,
SImon




--- On Sat, 30/3/13, peter dalgaard



wrote:


Huh?

This is utterly incomprehensible without

reading

the redhat

bugzilla, and even after reading, I'm not

sure

what

the

issue is. Something with bold Chinese

fonts in

X11,

but

maybe also affecting Latin fonts, ?

Please explain yourself.

-pd

On Mar 30, 2013, at 09:25 , Hin-Tak

Leung

wrote:



The problem was first seen with

R/Sweave

(#c0)

then

reproduced directly with cairo (#c10) and

was

eventually

traced to freetype. The 5-part bug fix:



610ee58e07090ead529849b2a454bb6c503b4995



da11e5e7647b668dee46fd0418ea5ecbc33ae3b2



e1a2ac1900f2f16ec48fb4840a6b7965a8373c2b



869fb8c49ddf292d6daf4826172a308973d3e11f



d56e544d653b09c657911629557ffc5277a503e3

was committed to freetype in January

and

will

form the

next release (2.4.12). They were back

ported

to

2.4.11

https://bugzilla.redhat.com/show_bug.cgi?id=891457#c35
and the redhat people had further

back-ported

it to

2.4.10 for fedora 18/19 (#c51).


The freetype people had reproduced

the

problem

with a

latin font, so th

Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread Dirk Eddelbuettel

On 3 September 2013 at 22:48, gianluca.mastranto...@yahoo.it wrote:
| Hi all
| 
| I have a R code that incorporates a C++ programm. I compiled the C++ 
| code with the following:
| 
| R CMD SHLIB   Model.cpp -Wall funzioni.cpp
| 
| it seems to work fine but when i run the R code i get this error message
| 
| Error in dyn.load(paste(dir_func, "Model.so", sep = "")) :
|unable to load shared object '/lustre/work/uuu/RCpp/Model.so':
|libR.so: cannot open shared object file: No such file or directory
| 
| I don't know how to fix it.
| The code is running on a cluster.

Qualified guess:  you ran R CMD SHLIB on the _central / master_ node, but not
the _compute_ nodes.   They never got the object file.

One more rigorous approach would be to wrap your function up in a package,
and have each compute node load the package.

Hope this helps,  Dirk

-- 
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com

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Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread Geoff Jentry

One problem is that i have not the privileges to install a package.


If you have a writable area you can install to there with the 
--library=LIB argument and then load the package using the lib.loc command.


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Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread Prof Brian Ripley

On 03/09/2013 23:04, Geoff Jentry wrote:

One problem is that i have not the privileges to install a package.


If you have a writable area you can install to there with the
--library=LIB argument and then load the package using the lib.loc command.


Actually, that will all happen automatically: package installation will 
create a personal library for you.  See e.g. ?.libPaths



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread gianluca.mastranto...@yahoo.it

Can you add some details?

Suppose i have the package Model.tar.gz and my writable are is in 
user/area, what i have to do next to install the package?


Il 04/09/13 00:04, Geoff Jentry ha scritto:

One problem is that i have not the privileges to install a package.


If you have a writable area you can install to there with the 
--library=LIB argument and then load the package using the lib.loc 
command.




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[Rd] libR.so: cannot open shared object file

2013-09-03 Thread gianluca.mastranto...@yahoo.it

Hi all

I have a R code that incorporates a C++ programm. I compiled the C++ 
code with the following:


R CMD SHLIB   Model.cpp -Wall funzioni.cpp

it seems to work fine but when i run the R code i get this error message

Error in dyn.load(paste(dir_func, "Model.so", sep = "")) :
  unable to load shared object '/lustre/work/uuu/RCpp/Model.so':
  libR.so: cannot open shared object file: No such file or directory

I don't know how to fix it.
The code is running on a cluster.

Thanks.

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Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread gianluca.mastranto...@yahoo.it

One problem is that i have not the privileges to install a package.


Il 03/09/13 23:14, Dirk Eddelbuettel ha scritto:

On 3 September 2013 at 22:48, gianluca.mastranto...@yahoo.it wrote:
| Hi all
|
| I have a R code that incorporates a C++ programm. I compiled the C++
| code with the following:
|
| R CMD SHLIB   Model.cpp -Wall funzioni.cpp
|
| it seems to work fine but when i run the R code i get this error message
|
| Error in dyn.load(paste(dir_func, "Model.so", sep = "")) :
|unable to load shared object '/lustre/work/uuu/RCpp/Model.so':
|libR.so: cannot open shared object file: No such file or directory
|
| I don't know how to fix it.
| The code is running on a cluster.

Qualified guess:  you ran R CMD SHLIB on the _central / master_ node, but not
the _compute_ nodes.   They never got the object file.

One more rigorous approach would be to wrap your function up in a package,
and have each compute node load the package.

Hope this helps,  Dirk



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