On Sat, Oct 23, 2010 at 2:49 AM, Rainer Hurling <rhur...@gwdg.de> wrote:
> On 22.10.2010 22:10 (UTC+1), Rainer Hurling wrote: > >> On 22.10.2010 16:18 (UTC+2), Rainer Hurling wrote: >> >>> On 22.10.2010 14:57 (UTC+1), Michael Lawrence wrote: >>> >>>> >>>> >>>> On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling <rhur...@gwdg.de >>>> <mailto:rhur...@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. >>> >> >> Ok, I am one step further now: >> >> >> (gdb) run >> Starting program: /usr/local/lib/R/bin/exec/R >> [..SNIP..] >> > library(RGtk2) >> [New LWP 100174] >> Breakpoint 2 at 0x318bd490: file Rgtk.c, line 104. >> Pending breakpoint "R_gtkInit" resolved >> [New Thread 2f408b00 (LWP 100174)] >> [Switching to Thread 2f408b00 (LWP 100174)] >> >> Breakpoint 2, R_gtkInit (rargc=0x30b11d10, rargv=0x30a98458, >> success=0x30afbad0) at Rgtk.c:104 >> 104 Rgtk.c: No such file or directory. >> in Rgtk.c >> (gdb) >> >> >> What do you suggest I should do next? >> > > Rgtk.c was not found from gdb because RGtk2 was not build with DEBUG=T and > R_KEEP_PKG_SOURCE=yes. > > So this is the next try. I can trace the code until it hangs: > > > library(RGtk2) > [New LWP 100250] > Breakpoint 2 at 0x458bd490: file Rgtk.c, line 104. > > Pending breakpoint "R_gtkInit" resolved > [New Thread 4322ef00 (LWP 100250)] > [Switching to Thread 4322ef00 (LWP 100250)] > > Breakpoint 2, R_gtkInit (rargc=0x446d0980, rargv=0x44698618, > success=0x446d09e0) at Rgtk.c:104 > 104 { > (gdb) n > 107 argc = (int) *rargc; > (gdb) n > 104 { > (gdb) n > 107 argc = (int) *rargc; > (gdb) n > 109 if (!gdk_display_get_default()) { > (gdb) n > 110 gtk_disable_setlocale(); > (gdb) n > 111 if (!gtk_init_check(&argc, &rargv)) { > (gdb) n > 121 if (!GDK_DISPLAY()) { > (gdb) n > 127 addInputHandler(R_InputHandlers, > ConnectionNumber(GDK_DISPLAY()), > (gdb) n > 132 if (!pipe(fds)) { > (gdb) n > 133 ifd = fds[0]; > (gdb) n > 134 ofd = fds[1]; > (gdb) n > 135 addInputHandler(R_InputHandlers, ifd, > R_gtk_timerInputHandler, 32); > (gdb) n > 133 ifd = fds[0]; > (gdb) n > 134 ofd = fds[1]; > (gdb) n > 135 addInputHandler(R_InputHandlers, ifd, > R_gtk_timerInputHandler, 32); > (gdb) n > 136 if (!g_thread_supported ()) g_thread_init (NULL); > (gdb) n > 137 g_thread_create(R_gtk_timerThreadFunc, NULL, FALSE, NULL); > (gdb) n > > Line 138 (R_CStackLimit = -1;) is hanging. It seems there is something > wrong with piping the file descriptor? > > > Thanks for looking into this. It looks like the g_thread_create line is hanging. I wonder if your version of GTK+/GLib is not built with threading support? But if that were the case, g_thread_init() should have aborted. You could try breaking on the R_gtk_timerThreadFunc just to see if the thread is executed at all or where it is hanging. Thanks again for taking the time to work on this. Sorry I have been non-responsive. Michael > 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 ... >>>> >>> > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
