[BioC] [Rd] R/Sweave/cairo/freetype bug fix.

Simon Urbanek simon.urbanek at r-project.org
Mon Apr 1 14:54:44 CEST 2013


On Apr 1, 2013, at 5:18 AM, Hin-Tak Leung wrote:

> --- On Sat, 30/3/13, Hin-Tak Leung <htl10 at users.sourceforge.net> 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.
> 

That is not "the official bundle" - that is merely a convenience binary for the Cairo package (not to be confused with cairo back-end in R) for users that don't have cairographics installed on their system. I don't think that CRAN uses this for R builds.


> 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.
> 

But then why would even the old binary in the Cairo package be an issue? It uses Win32 API, not freetype.

Cheers,
Simon



>> ------------------------------
>> 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 <pdalgd at gmail.com>
>> 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 this affects most people, unlike
>> what the
>>>> initial report (#c0) suggests.
>>>>> 
>>>>> Since freetype is part of X11, most unix/linux
>> users
>>>> would be understandably nervous about breaking X
>> (see #c45
>>>> for screenshot of broken gnome terminal!) and
>> should wait up
>>>> to a year before the new and not-yet-released
>> 2.4.12 becomes
>>>> an official upgrade; or contact their favourite
>> unix vendors
>>>> and/or Apple for upgrades. AFAIK, current
>> up-to-date linux
>>>> distributions ships the rather older 2.4.10, with
>> the
>>>> exception of fedora 18/19 (#c51). Mac OS X 10.5
>> ships
>>>> freetype 2.3.5 as part of X11; I haven't bother
>> looking up
>>>> later Mac OS X's.
>>>>> 
>>>>> The official R binaries for windows and mac OS
>> X are
>>>> compiled against static libraries of cairo 1.10.2
>> (over 2
>>>> years old), and cairo 1.11.2 and freetype 2.4.4
>>>> respectively, and are firmly in the "do not work
>> correctly"
>>>> category.
>>>>> 
>>>>> The long and short of the story is that
>> R/Sweave uses a
>>>> feature of cairo which wasn't implemented before
>> cairo
>>>> 1.11.2 (#c13, Jan 2011), which in turn depends on a
>> feature
>>>> of freetype that has been around since 2005 but did
>> not
>>>> anticipate cairo's usage. It is commendable that
>> the
>>>> freetype people did not refer to cairo's usage as
>> "misuse"
>>>> but took the patience to address the problem,
>> unlike some
>>>> group's style.
>>>>> 
>>>>> It has been an interesting few months returning
>> to
>>>> freetype after about 17 years, I think.
>>>>> 
>>>>> Here is how to look up what version of freetype
>> -
>>>> libfreetype.so.x.y.z for most unix platforms, and
>>>> /usr/X11/lib/libfreetype.x.y.z.dylib on Mac OS X:
>>>>> 
>>>>> (excerpt from docs/VERSION.DLL)
>>>>> 
>>>>>       version   
>>>> x.y.z   date of release
>>>>>       2.4.11 
>>>>     6.10.0  Dec 2012
>>>>>       2.4.10 
>>>>     6.9.0   June 2012
>>>>>       2.4.9 
>>    
>>>> 6.8.1   March 2012
>>>>> ...
>>>>>       2.4.4 
>>    
>>>> 6.6.2   Nov 2010  (official R
>> mac
>>>> binaries)
>>>>> ...
>>>>>       2.3.5 
>>    
>>>> 6.3.16  July 2007 (Mac OS X 10.5)
>>>>> 
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org
>>>> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> -- 
>>>> Peter Dalgaard, Professor,
>>>> Center for Statistics, Copenhagen Business School
>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>> Phone: (+45)38153501
>>>> Email: pd.mes at cbs.dk 
>>>> Priv: PDalgd at gmail.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ______________________________________________
>>>> R-devel at r-project.org
>> mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> 
>>> 
>> 
>> 
> 
> 



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