Multiple platform build/check report for BioC 3.9 - CHECK report for HilbertVisGUI on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:HilbertVisGUI.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HilbertVisGUI_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HilbertVisGUI.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HilbertVisGUI/DESCRIPTION' ... OK
* this is package 'HilbertVisGUI' version '1.42.0'
* 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 whether package 'HilbertVisGUI' can be installed ... OK
* 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 ... WARNING
---- unloading
* 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 ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -mms-bitfields
Non-portable flags in variable 'PKG_CFLAGS':
  -mms-bitfields
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/HilbertVisGUI/libs/x64/HilbertVisGUI.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
hilbertDisplay  0.3   1.25   78.88
* 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: 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/HilbertVisGUI.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch HilbertVisGUI
###
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'HilbertVisGUI' ...
** using staged installation

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   WARNING: this package has a configure script
         It probably needs manual configuration
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** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"  -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS   -O2 -Wall  -std=gnu99 -mtune=generic -c R_env_prot.c -o R_env_prot.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_interface.cc -o R_interface.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/include/R.h:91:0,
                 from R_interface.cc:17:
C:/Users/biocbuild/bbs-3.9-bioc/R/include/R_ext/RS.h:55:0: warning: "ERROR" redefined
 #define ERROR   ),error(R_problem_buf);}
 ^
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/windows.h:71:0,
                 from R_interface.cc:13:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/wingdi.h:75:0: note: this is the location of the previous definition
 #define ERROR 0
 ^
R_interface.cc: In function 'SEXPREC* R_display_hilbert(SEXP)':
R_interface.cc:510:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int i = 0; i < palette_steps->size(); i++ )
                      ^
R_interface.cc:509:11: warning: unused variable 'palette_level' [-Wunused-variable]
    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 between signed and unsigned integer expressions [-Wsign-compare]
    for( int i = 0; i < palette_steps->size(); i++ )
                      ^
R_interface.cc: In member function 'double RDataVector::get_bin_value(long int, long int) const [with data_el_t = int]':
R_interface.cc:135:9: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if( INTEGER(data)[i] < val )
         ^
R_interface.cc: In member function 'double RDataVector::get_bin_value(long int, long int) const [with data_el_t = double]':
R_interface.cc:196:9: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized]
         if( REAL(data)[i] < val )
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c colorizers.cc -o colorizers.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c display.cc -o display.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ruler.cc -o ruler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -mms-bitfields -IC:/gtkmm64/include/gtkmm-2.4 -IC:/gtkmm64/lib/gtkmm-2.4/include -IC:/gtkmm64/include/atkmm-1.6 -IC:/gtkmm64/include/giomm-2.4 -IC:/gtkmm64/lib/giomm-2.4/include -IC:/gtkmm64/include/pangomm-1.4 -IC:/gtkmm64/lib/pangomm-1.4/include -IC:/gtkmm64/include/gtk-2.0 -IC:/gtkmm64/include/gdkmm-2.4 -IC:/gtkmm64/lib/gdkmm-2.4/include -IC:/gtkmm64/include/atk-1.0 -IC:/gtkmm64/include/glibmm-2.4 -IC:/gtkmm64/lib/glibmm-2.4/include -IC:/gtkmm64/include/glib-2.0 -IC:/gtkmm64/lib/glib-2.0/include -IC:/gtkmm64/include/sigc++-2.0 -IC:/gtkmm64/lib/sigc++-2.0/include -IC:/gtkmm64/include/cairomm-1.0 -IC:/gtkmm64/lib/cairomm-1.0/include -IC:/gtkmm64/include/pango-1.0 -IC:/gtkmm64/include/cairo -IC:/gtkmm64/include -IC:/gtkmm64/include/freetype2 -IC:/gtkmm64/include/libpng14 -IC:/gtkmm64/lib/gtk-2.0/include -IC:/gtkmm64/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c window.cc -o window.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o HilbertVisGUI.dll tmp.def R_env_prot.o R_interface.o colorizers.o display.o ruler.o window.o -LC:/gtkmm64/lib -Lc:/devel/dist/win64/libpng-1.4.3-1/lib -lgtkmm-2.4 -latkmm-1.6 -lgdkmm-2.4 -lgiomm-2.4 -lpangomm-1.4 -lgtk-win32-2.0 -lglibmm-2.4 -lcairomm-1.0 -lsigc-2.0 -lgdk-win32-2.0 -latk-1.0 -lgio-2.0 -lpangowin32-1.0 -lgdi32 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lpng14 -lpango-1.0 -lcairo -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lintl -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.9-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/R/library/00LOCK-HilbertVisGUI/00new/HilbertVisGUI/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HilbertVisGUI'
    finding HTML links ... done
    dotsapply                               html  
    hilbertDisplay                          html  
    hilbertDisplayThreeChannel              html  
    simpleLinPlot                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HilbertVisGUI)
Making 'packages.html' ... done

CHECK report for HilbertVisGUI on tokay2

Summary

Command output

Installation output

Tests output

Example timings