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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the HilbertVisGUI package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 863/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HilbertVisGUI 1.50.0 (landing page) Simon Anders
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| Package: HilbertVisGUI |
| Version: 1.50.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HilbertVisGUI_1.50.0.tar.gz |
| StartedAt: 2021-10-14 10:10:45 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:11:01 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 16.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HilbertVisGUI.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HilbertVisGUI_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/HilbertVisGUI.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HilbertVisGUI/DESCRIPTION’ ... OK
* this is package ‘HilbertVisGUI’ version ‘1.50.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 [-Wdeprecated-declarations]
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-3.13-bioc/meat/HilbertVisGUI.Rcheck/00install.out’ for details.
* 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 R 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/HilbertVisGUI.Rcheck/00check.log’
for details.
HilbertVisGUI.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HilbertVisGUI
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)
HilbertVisGUI.Rcheck/HilbertVisGUI-Ex.timings
| name | user | system | elapsed | |
| hilbertDisplay | 0.067 | 0.015 | 0.088 | |