Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 959/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HilbertVisGUI 1.65.0 (landing page) Simon Anders
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
Package: HilbertVisGUI |
Version: 1.65.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HilbertVisGUI_1.65.0.tar.gz |
StartedAt: 2024-12-23 22:52:47 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:53:05 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 18.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: HilbertVisGUI.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HilbertVisGUI.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HilbertVisGUI_1.65.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HilbertVisGUI.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘1.65.0’ * 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: 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-3.21-bioc/meat/HilbertVisGUI.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... INFO 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: ‘SET_TYPEOF’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/HilbertVisGUI.Rcheck/00check.log’ for details.
HilbertVisGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HilbertVisGUI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 `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-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c R_interface.cc -o R_interface.o R_interface.cc:16: warning: "R_NO_REMAP" redefined 16 | #define R_NO_REMAP | <command-line>: 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<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-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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)
HilbertVisGUI.Rcheck/HilbertVisGUI-Ex.timings
name | user | system | elapsed | |
hilbertDisplay | 0.089 | 0.021 | 0.118 | |