R help - Oct 2010 - R-2.12.0 hangs while installing some packages on FreeBSD

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.

Thanks in advance,
Rainer Hurling

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.
>
> Thanks in advance,
> Rainer Hurling
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at 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, UK                Fax:  +44 1865 272595

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 ...

[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?
> 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 ...