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###
### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL HilbertVisGUI
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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-3.14-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-3.14-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<PixbufAnimationIter> 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> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
42 | std::auto_ptr<DataVector> 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<typename> 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<double>::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<double>::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<data_el_t>::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<data_el_t>::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-3.14-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<PixbufAnimationIter> 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> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
42 | std::auto_ptr<DataVector> 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<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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<PixbufAnimationIter> 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<<lv) - 1 - c.y, ( 1l << (lv-1) ) - 1 - c.x }; }
| ~~~~~~~~~~~~~^~~~~
display.cc:23:78: warning: narrowing conversion of ‘(((1 << (lv - 1)) - 1) - ((long int)c.coord::x))’ from ‘long int’ to ‘int’ [-Wnarrowing]
23 | case 3: { return (coord) { (1l<<lv) - 1 - c.y, ( 1l << (lv-1) ) - 1 - c.x }; }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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 ruler.cc -o ruler.o
In file included from /usr/include/gdkmm-2.4/gdkmm.h:34,
from /usr/include/gtkmm-2.4/gtkmm.h:89,
from ruler.h:4,
from ruler.cc:6:
/usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
124 | Glib::RefPtr<PixbufAnimationIter> 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-3.14-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<PixbufAnimationIter> 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> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
42 | std::auto_ptr<DataVector> 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<typename> 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-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)
