[Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
Rainer Hurling
rhurlin at gwdg.de
Fri Oct 22 16:18:51 CEST 2010
On 22.10.2010 14:57 (UTC+1), Michael Lawrence wrote:
>
>
> On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling <rhurlin at gwdg.de
> <mailto: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.
Michael, thank you for answering. As I wrote earlier (on R-help@),
unfortunately I have no experience with debugging (I am not a
programmer). So I would need some more assistence.
Is there a difference between 'library(RGtk2)' and 'dyn.load(RGtk2)' in
initializing GTK+? I am able to dyn.load, but library does not work.
After starting with 'R -d gdb' is the following right?
(gdb) break R_gtkInit
Function "R_gtkInit" not defined.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 1 (R_gtkInit) pending.
When I try to proceed, it gives me the following message
(gdb) run
Starting program: /usr/local/lib/R/bin/exec/R
/libexec/ld-elf.so.1: Shared object "libRblas.so" not found,
required by "R"
Program exited with code 01.
Obviously there is some wrong with my try?
Thanks again,
Rainer
> 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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