[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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