############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HilbertVisGUI ### ############################################################################## ############################################################################## * checking for file ‘HilbertVisGUI/DESCRIPTION’ ... OK * preparing ‘HilbertVisGUI’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * 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 using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/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 -Werror=format-security -c R_env_prot.c -o R_env_prot.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c R_interface.cc -o R_interface.o R_interface.cc:16:9: warning: "R_NO_REMAP" redefined 16 | #define R_NO_REMAP | ^~~~~~~~~~ : note: this is the location of the previous definition 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:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glibmm-2.4/glibmm/thread.h:39, from /usr/include/glibmm-2.4/glibmm.h:103, from /usr/include/gtkmm-2.4/gtkmm.h:87: /usr/include/glib-2.0/glib/gtypes.h:578:26: note: declared here 578 | 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: /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:26, from /usr/include/glib-2.0/gobject/gbinding.h:31, from /usr/include/glib-2.0/glib-object.h:24, 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: /usr/include/glib-2.0/gobject/gtype.h:729:3: note: declared here 729 | } GTypeDebugFlags GOBJECT_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: /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations] 73 | GTimeVal last_popdown; | ^~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtypes.h:578:26: note: declared here 578 | 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: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 42 | std::auto_ptr data; | ^~~~~~~~ In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/memory:78, 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:107: /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here 59 | 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:529:20: error: format not a string literal and no format arguments [-Werror=format-security] 529 | Rf_error( buf ); | ^~~ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ cc1plus: some warnings being treated as errors make: *** [/home/biocbuild/R/R/etc/Makeconf:202: R_interface.o] Error 1 ERROR: compilation failed for package ‘HilbertVisGUI’ * removing ‘/home/biocbuild/tmp/RtmpoURrqA/Rinst9a38526ccdb4b/HilbertVisGUI’ ----------------------------------- ERROR: package installation failed