############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL HilbertVisGUI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘HilbertVisGUI’ ... ** using staged installation Checking for pkg-config... /usr/bin/pkg-config Checking for gtkmm-2.4... found: version 2.24.5 ** libs gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -fpic -g -O2 -Wall -c R_env_prot.c -o R_env_prot.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -fpic -g -O2 -Wall -c R_interface.cc -o R_interface.o In file included from /usr/include/gdkmm-2.4/gdkmm.h:34, from /usr/include/gtkmm-2.4/gtkmm.h:89, from display.h:7, from R_interface.cc:8: /usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 124 | Glib::RefPtr get_iter(const GTimeVal* start_time); | ^ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from R_interface.cc:8: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37, from /usr/include/gtk-2.0/gtk/gtkwidget.h:36, from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35, from /usr/include/gtk-2.0/gtk/gtkbin.h:35, from /usr/include/gtk-2.0/gtk/gtkwindow.h:36, from /usr/include/gtk-2.0/gtk/gtkdialog.h:35, from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:33, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from display.h:7, from R_interface.cc:8: /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations] 236 | void gtk_type_init (GTypeDebugFlags debug_flags); | ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:22, from /usr/include/glibmm-2.4/glibmm/value.h:24, from /usr/include/glibmm-2.4/glibmm/error.h:22, from /usr/include/glibmm-2.4/glibmm/thread.h:48, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from R_interface.cc:8: /usr/include/glib-2.0/gobject/gtype.h:685:3: note: declared here 685 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36; | ^~~~~~~~~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31, from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtk.h:126, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from display.h:7, from R_interface.cc:8: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from R_interface.cc:8: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from R_interface.cc:10: colorizers.h:42:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | std::auto_ptr data; | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /usr/include/glibmm-2.4/glibmm/variant.h:33, from /usr/include/glibmm-2.4/glibmm/containerhandle_shared.h:23, from /usr/include/glibmm-2.4/glibmm/arrayhandle.h:21, from /usr/include/glibmm-2.4/glibmm.h:92, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from R_interface.cc:8: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ R_interface.cc: In function ‘SEXPREC* R_display_hilbert(SEXP)’: R_interface.cc:510:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 510 | for( int i = 0; i < palette_steps->size(); i++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ R_interface.cc:509:11: warning: unused variable ‘palette_level’ [-Wunused-variable] 509 | double palette_level = log( REAL( max_palette_valueR )[ 0 ] ) / log( 10. ) * 4; | ^~~~~~~~~~~~~ R_interface.cc: In member function ‘void MainWindowForRForBidir::set_palette_level(double)’: R_interface.cc:702:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 702 | for( int i = 0; i < palette_steps->size(); i++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ R_interface.cc: In member function ‘double RDataVector::get_bin_value(long int, long int) const [with data_el_t = int]’: R_interface.cc:119:8: warning: ‘val’ may be used uninitialized in this function [-Wmaybe-uninitialized] 119 | int val; | ^~~ R_interface.cc: In member function ‘double RDataVector::get_bin_value(long int, long int) const [with data_el_t = double]’: R_interface.cc:219:11: warning: ‘val’ may be used uninitialized in this function [-Wmaybe-uninitialized] 219 | val /= count; | ~~~~^~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -fpic -g -O2 -Wall -c colorizers.cc -o colorizers.o In file included from /usr/include/gdkmm-2.4/gdkmm.h:34, from /usr/include/gtkmm-2.4/gtkmm.h:89, from colorizers.h:6, from colorizers.cc:1: /usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 124 | Glib::RefPtr get_iter(const GTimeVal* start_time); | ^ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from colorizers.h:6, from colorizers.cc:1: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37, from /usr/include/gtk-2.0/gtk/gtkwidget.h:36, from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35, from /usr/include/gtk-2.0/gtk/gtkbin.h:35, from /usr/include/gtk-2.0/gtk/gtkwindow.h:36, from /usr/include/gtk-2.0/gtk/gtkdialog.h:35, from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:33, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from colorizers.h:6, from colorizers.cc:1: /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations] 236 | void gtk_type_init (GTypeDebugFlags debug_flags); | ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:22, from /usr/include/glibmm-2.4/glibmm/value.h:24, from /usr/include/glibmm-2.4/glibmm/error.h:22, from /usr/include/glibmm-2.4/glibmm/thread.h:48, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from colorizers.h:6, from colorizers.cc:1: /usr/include/glib-2.0/gobject/gtype.h:685:3: note: declared here 685 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36; | ^~~~~~~~~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31, from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtk.h:126, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from colorizers.h:6, from colorizers.cc:1: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from colorizers.h:6, from colorizers.cc:1: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from colorizers.cc:1: colorizers.h:42:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | std::auto_ptr data; | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from colorizers.h:4, from colorizers.cc:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -fpic -g -O2 -Wall -c display.cc -o display.o In file included from /usr/include/gdkmm-2.4/gdkmm.h:34, from /usr/include/gtkmm-2.4/gtkmm.h:89, from display.h:7, from display.cc:1: /usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 124 | Glib::RefPtr get_iter(const GTimeVal* start_time); | ^ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from display.cc:1: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37, from /usr/include/gtk-2.0/gtk/gtkwidget.h:36, from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35, from /usr/include/gtk-2.0/gtk/gtkbin.h:35, from /usr/include/gtk-2.0/gtk/gtkwindow.h:36, from /usr/include/gtk-2.0/gtk/gtkdialog.h:35, from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:33, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from display.h:7, from display.cc:1: /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations] 236 | void gtk_type_init (GTypeDebugFlags debug_flags); | ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:22, from /usr/include/glibmm-2.4/glibmm/value.h:24, from /usr/include/glibmm-2.4/glibmm/error.h:22, from /usr/include/glibmm-2.4/glibmm/thread.h:48, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from display.cc:1: /usr/include/glib-2.0/gobject/gtype.h:685:3: note: declared here 685 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36; | ^~~~~~~~~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31, from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtk.h:126, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from display.h:7, from display.cc:1: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from display.h:7, from display.cc:1: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ display.cc: In function ‘coord hilbert(long long int, int)’: display.cc:21:46: warning: narrowing conversion of ‘(((long int)c.coord::y) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing] 21 | case 1: { return (coord) { c.x, c.y + ( 1l << (lv-1) ) }; } | ~~~~^~~~~~~~~~~~~~~~~~ display.cc:22:41: warning: narrowing conversion of ‘(((long int)c.coord::x) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing] 22 | case 2: { return (coord) { c.x + ( 1l << (lv-1) ), c.y + ( 1l << (lv-1) ) }; } | ~~~~^~~~~~~~~~~~~~~~~~ display.cc:22:65: warning: narrowing conversion of ‘(((long int)c.coord::y) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing] 22 | case 2: { return (coord) { c.x + ( 1l << (lv-1) ), c.y + ( 1l << (lv-1) ) }; } | ~~~~^~~~~~~~~~~~~~~~~~ display.cc:23:50: warning: narrowing conversion of ‘(((1 << lv) - 1) - ((long int)c.coord::y))’ from ‘long int’ to ‘int’ [-Wnarrowing] 23 | case 3: { return (coord) { (1l< get_iter(const GTimeVal* start_time); | ^ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from ruler.h:4, from ruler.cc:6: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37, from /usr/include/gtk-2.0/gtk/gtkwidget.h:36, from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35, from /usr/include/gtk-2.0/gtk/gtkbin.h:35, from /usr/include/gtk-2.0/gtk/gtkwindow.h:36, from /usr/include/gtk-2.0/gtk/gtkdialog.h:35, from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:33, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from ruler.h:4, from ruler.cc:6: /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations] 236 | void gtk_type_init (GTypeDebugFlags debug_flags); | ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:22, from /usr/include/glibmm-2.4/glibmm/value.h:24, from /usr/include/glibmm-2.4/glibmm/error.h:22, from /usr/include/glibmm-2.4/glibmm/thread.h:48, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from ruler.h:4, from ruler.cc:6: /usr/include/glib-2.0/gobject/gtype.h:685:3: note: declared here 685 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36; | ^~~~~~~~~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31, from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtk.h:126, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from ruler.h:4, from ruler.cc:6: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from ruler.h:4, from ruler.cc:6: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -fpic -g -O2 -Wall -c window.cc -o window.o In file included from /usr/include/gdkmm-2.4/gdkmm.h:34, from /usr/include/gtkmm-2.4/gtkmm.h:89, from window.h:5, from window.cc:4: /usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 124 | Glib::RefPtr get_iter(const GTimeVal* start_time); | ^ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from window.h:5, from window.cc:4: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37, from /usr/include/gtk-2.0/gtk/gtkwidget.h:36, from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35, from /usr/include/gtk-2.0/gtk/gtkbin.h:35, from /usr/include/gtk-2.0/gtk/gtkwindow.h:36, from /usr/include/gtk-2.0/gtk/gtkdialog.h:35, from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:33, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from window.h:5, from window.cc:4: /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations] 236 | void gtk_type_init (GTypeDebugFlags debug_flags); | ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:22, from /usr/include/glibmm-2.4/glibmm/value.h:24, from /usr/include/glibmm-2.4/glibmm/error.h:22, from /usr/include/glibmm-2.4/glibmm/thread.h:48, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from window.h:5, from window.cc:4: /usr/include/glib-2.0/gobject/gtype.h:685:3: note: declared here 685 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36; | ^~~~~~~~~~~~~~~ In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31, from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30, from /usr/include/gtk-2.0/gtk/gtk.h:126, from /usr/include/gtkmm-2.4/gtkmm/box.h:44, from /usr/include/gtkmm-2.4/gtkmm.h:91, from window.h:5, from window.cc:4: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/galloca.h:32, from /usr/include/glib-2.0/glib.h:30, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:88, from /usr/include/gtkmm-2.4/gtkmm.h:87, from window.h:5, from window.cc:4: /usr/include/glib-2.0/glib/gtypes.h:545:26: note: declared here 545 | typedef struct _GTimeVal GTimeVal GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime); | ^~~~~~~~ In file included from window.cc:7: colorizers.h:42:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | std::auto_ptr data; | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /usr/include/glibmm-2.4/glibmm/variant.h:33, from /usr/include/glibmm-2.4/glibmm/containerhandle_shared.h:23, from /usr/include/glibmm-2.4/glibmm/arrayhandle.h:21, from /usr/include/glibmm-2.4/glibmm.h:92, from /usr/include/gtkmm-2.4/gtkmm.h:87, from window.h:5, from window.cc:4: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ window.cc: In member function ‘virtual void MainWindow::on_btnZoomOut4x_clicked()’: window.cc:212:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=] 212 | } catch( HilbertValueError e ) { | ^ window.cc: In member function ‘virtual void MainWindow::on_btnCoarser_clicked()’: window.cc:232:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=] 232 | } catch( HilbertValueError e ) { | ^ window.cc: In member function ‘virtual void MainWindow::on_btnFiner_clicked()’: window.cc:241:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=] 241 | } catch( HilbertValueError e ) { | ^ window.cc: In member function ‘virtual void MainWindow::on_canvasClicked(GdkEventButton*, long int, long int)’: window.cc:371:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=] 371 | } catch (HilbertValueError e) { | ^ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o HilbertVisGUI.so R_env_prot.o R_interface.o colorizers.o display.o ruler.o window.o -lgtkmm-2.4 -latkmm-1.6 -lgtk-x11-2.0 -lgdkmm-2.4 -lgiomm-2.4 -lpangomm-1.4 -lglibmm-2.4 -lcairomm-1.0 -lsigc-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lfontconfig -lfreetype -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-HilbertVisGUI/00new/HilbertVisGUI/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HilbertVisGUI)