Multiple platform build/check report for BioC 3.20 - CHECK results for HilbertVisGUI on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for HilbertVisGUI on nebbiolo2

To the developers/maintainers of the HilbertVisGUI package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HilbertVisGUI.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: HilbertVisGUI

Version: 1.64.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HilbertVisGUI_1.64.0.tar.gz

StartedAt: 2024-11-29 01:10:52 -0500 (Fri, 29 Nov 2024)

EndedAt: 2024-11-29 01:14:50 -0500 (Fri, 29 Nov 2024)

EllapsedTime: 238.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: HilbertVisGUI.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HilbertVisGUI_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HilbertVisGUI.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HilbertVisGUI/DESCRIPTION’ ... OK
* this is package ‘HilbertVisGUI’ version ‘1.64.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HilbertVisGUI’ can be installed ... WARNING
Found the following significant warnings:
  /usr/include/gdkmm-2.4/gdkmm/pixbufanimation.h:124:72: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
  colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  R_interface.cc:529:20: warning: format not a string literal and no format arguments [-Wformat-security]
  display.cc:21:46: warning: narrowing conversion of ‘(((long int)c.coord::y) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing]
  display.cc:22:41: warning: narrowing conversion of ‘(((long int)c.coord::x) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing]
  display.cc:22:65: warning: narrowing conversion of ‘(((long int)c.coord::y) + (1 << (lv - 1)))’ from ‘long int’ to ‘int’ [-Wnarrowing]
  display.cc:23:50: warning: narrowing conversion of ‘(((1 << lv) - 1) - ((long int)c.coord::y))’ from ‘long int’ to ‘int’ [-Wnarrowing]
  display.cc:23:78: warning: narrowing conversion of ‘(((1 << (lv - 1)) - 1) - ((long int)c.coord::x))’ from ‘long int’ to ‘int’ [-Wnarrowing]
  window.cc:212:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=]
  window.cc:232:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=]
  window.cc:241:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=]
  window.cc:371:31: warning: catching polymorphic type ‘class HilbertValueError’ by value [-Wcatch-value=]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/HilbertVisGUI.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hilbertDisplay: no visible global function definition for
  ‘colorRampPalette’
hilbertDisplay: no visible global function definition for ‘col2rgb’
hilbertDisplay: no visible global function definition for ‘median’
hilbertDisplayThreeChannel: no visible global function definition for
  ‘col2rgb’
Undefined global functions or variables:
  col2rgb colorRampPalette median
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette")
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘HilbertVisGUI/libs/HilbertVisGUI.so’:
  Found non-API call to R: ‘getInputHandler’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/HilbertVisGUI.Rcheck/00check.log’
for details.

Installation output

HilbertVisGUI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HilbertVisGUI
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-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++17 -I"/home/biocbuild/bbs-3.20-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: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:731:3: note: declared here
  731 | } 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> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   42 |    std::auto_ptr<DataVector> data;
      |         ^~~~~~~~
In file included from /usr/include/c++/13/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:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:529:20: warning: format not a string literal and no format arguments [-Wformat-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<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  702 |    for( int i = 0; i < palette_steps->size(); i++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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: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:731:3: note: declared here
  731 | } 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);
      |                          ^~~~~~~~
colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   42 |    std::auto_ptr<DataVector> data;
      |         ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from colorizers.h:4:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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: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:731:3: note: declared here
  731 | } 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);
      |                          ^~~~~~~~
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++17 -I"/home/biocbuild/bbs-3.20-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: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:731:3: note: declared here
  731 | } 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);
      |                          ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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: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:731:3: note: declared here
  731 | } 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 window.cc:7:
colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   42 |    std::auto_ptr<DataVector> data;
      |         ^~~~~~~~
In file included from /usr/include/c++/13/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:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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++17 -shared -L/home/biocbuild/bbs-3.20-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 -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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

Example timings

HilbertVisGUI.Rcheck/HilbertVisGUI-Ex.timings

name	user	system	elapsed
hilbertDisplay	0.084	0.017	0.103