Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling 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. 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
Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
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. 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
Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
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? 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
Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
[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 ... __
