Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD from Michael Lawrence on 2010-10-22 (R devel archive)

Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD

From: Michael Lawrence <lawrence.michael_at_gene.com>
Date: Fri, 22 Oct 2010 05:57:24 -0700

On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling <rhurlin_at_gwdg.de> wrote:

> [moved from R-help]
>
> On 21.10.2010 18:09 (UTC+1), Prof Brian Ripley wrote:
>
>> If you do R CMD INSTALL --no-test-load this will skip the part that is
>> hanging and you can try loading in stages (e.g. dyn.load on the RGtk2.so).
>>
>
> With '--no-test-load' it installs and ends normal. Loading per
> dyn.load("RGtk2.so") works, just as dyn.load("RGtk2.so",F) and
> dyn.load("RGtk2.so",,F). Unloading works, too.
>
> Normal loading over library(RGtk2) within R does not work. R than is
> hanging.
>
> It seems the problem is not with the library itself?
>
>
It looks like something is happening when initializing GTK+ and the event loop. This happens in the function R_gtkInit in Rgtk.c. If you could run R -d gdb and break on that function, perhaps you could step through until it hangs.

Thanks,
Michael

> I think this is rather technical for R-help, so maybe move to R-devel?
>>
>
> I moved to R-devel.
>
> And can you check the RGtk2 version? A recent but not current version
>> (2.12.17?) did hang initializing Gtk+ on some platforms and Michael
>> Lawrence had to be involved.
>>
>
> I am using RGtk2_2.12.18.tar.gz for month now.
>
>
> On Thu, 21 Oct 2010, Rainer Hurling wrote:
>>
>> Am 21.10.2010 16:12 (UTC+1) schrieb Prof Brian Ripley:
>>>
>>>> On Thu, 21 Oct 2010, Rainer Hurling wrote:
>>>>
>>>> I am working with R-2.12.0 on FreeBSD 9.0-CURRENT for a while now. I
>>>>> successfully installed more than 300 packages (most as dependencies of
>>>>> others).
>>>>>
>>>>> There are two packages I am not able to install: RGtk2 and rggobi.
>>>>>
>>>>> For example rggobi builds fine and after that it wants to load:
>>>>>
>>>>> ------------------------------------------------------
>>>>> # R CMD INSTALL rggobi_2.1.16.tar.gz
>>>>> [..SNIP..]
>>>>> gcc -std=gnu99 -shared -L/usr/local/lib -o rggobi.so RSEval.o brush.o
>>>>> colorSchemes.o conversion.o data.o dataset.o display.o displays.o
>>>>> edges.o ggobi.o identify.o init.o io.o keyHandlers.o longitudinal.o
>>>>> modes.o plot.o plots.o plugins.o print.o session.o smooth.o ui.o
>>>>> utils.o -pthread -L/usr/local/lib -lggobi -lgtk-x11-2.0 -lxml2
>>>>> -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext
>>>>> -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage
>>>>> -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm
>>>>> -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0
>>>>> -lglib-2.0
>>>>> installiert nach /usr/local/lib/R/library/rggobi/libs
>>>>> ** R
>>>>> ** data
>>>>> ** moving datasets to lazyload DB
>>>>> ** demo
>>>>> ** preparing package for lazy loading
>>>>> ------------------------------------------------------
>>>>>
>>>>> At this point the install process is hanging, R utilises no more CPU
>>>>> time. Same with package RGtk2.
>>>>>
>>>>> Is this a known error? Please let me know if I can give more
>>>>> information or try something different.
>>>>>
>>>>
>>>> Well, those are exactly the two packages using Gtk+.
>>>>
>>>> There is no known general problem, and as you could have checked from
>>>> the CRAN check pages, those packages install without problems on several
>>>> platforms. (Not Solaris, where ggobi does not install and RGtk2 requires
>>>> gcc, and not x64 Windows where both need to be patched.)
>>>>
>>>> So it does look very like there is a problem with loading against the
>>>> Gtk+ system libraries on your system.
>>>>
>>>
>>> I think you are right. With previous versions of R (until R-2.10.x) I
>>> did not have this hanging when loading RGtk2 ... And I am pretty sure
>>> that I have no problems with gtk2 outside of R on my FreeBSD system.
>>>
>>> In the meantime I found out that the reported loading error of rggobi
>>> is a loading error of RGtk2, which fails (hangs). So there remains
>>> only a loading error with RGtk2. (Because of that I changed the subject.)
>>>
>>> After building/installing RGtk2, there are the following messages:
>>>
>>> ------------------------------------------------------
>>> [..SNIP..]
>>> gcc -std=gnu99 -shared -L/usr/local/lib -o RGtk2.so RGtkDataFrame.o
>>> Rgtk.o atkAccessors.o atkClasses.o atkConversion.o atkFuncs.o
>>> atkManuals.o atkUserFuncs.o cairo-enums.o cairoAccessors.o
>>> cairoConversion.o cairoFuncs.o cairoManuals.o cairoUserFuncs.o
>>> classes.o conversion.o eventLoop.o gdkAccessors.o gdkClasses.o
>>> gdkConversion.o gdkFuncs.o gdkManuals.o gdkUserFuncs.o glib.o
>>> gobject.o gtkAccessors.o gtkClasses.o gtkConversion.o gtkFuncs.o
>>> gtkManuals.o gtkUserFuncs.o libgladeAccessors.o libgladeFuncs.o
>>> libgladeManuals.o libgladeUserFuncs.o pangoAccessors.o pangoClasses.o
>>> pangoConversion.o pangoFuncs.o pangoManuals.o pangoUserFuncs.o utils.o
>>> zcompat.o -pthread -L/usr/local/lib -lglade-2.0 -lgtk-x11-2.0 -lxml2
>>> -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext
>>> -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage
>>> -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm
>>> -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0
>>> -lglib-2.0 -pthread -L/usr/local/lib -lgthread-2.0 -lglib-2.0
>>> installiert nach /usr/local/lib/R/library/RGtk2/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices ...
>>> ** testing if installed package can be loaded [..hanging from here..]
>>> ------------------------------------------------------
>>>
>>> Is there a chance to find out what is wrong with loading RGtk2 on my
>>> system? Unfortunately I have almost no experience with real debugging
>>> methods on R. But of course I am willing to help and try out ...
>>>
>>
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