BioC 3.5: INSTALL report for HilbertVisGUI on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL HilbertVisGUI
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘HilbertVisGUI’ ...
Checking for pkg-config... /usr/bin/pkg-config
Checking for gtkmm-2.4... found: version 2.24.4
** libs
gcc -I/home/biocbuild/bbs-3.5-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
cc1: warning: command line option ‘-std=c++11’ is valid for C++/ObjC++ but not for C
cc1: warning: command line option ‘-std=c++11’ is valid for C++/ObjC++ but not for C
g++  -I/home/biocbuild/bbs-3.5-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 R_interface.cc:10:0:
colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
    std::auto_ptr<DataVector> data;
         ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /usr/include/glibmm-2.4/glibmm/objectbase.h:32,
                 from /usr/include/glibmm-2.4/glibmm/wrap.h:23,
                 from /usr/include/glibmm-2.4/glibmm/containerhandle_shared.h:26,
                 from /usr/include/glibmm-2.4/glibmm/arrayhandle.h:23,
                 from /usr/include/glibmm-2.4/glibmm.h:91,
                 from /usr/include/gtkmm-2.4/gtkmm.h:87,
                 from display.h:7,
                 from R_interface.cc:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
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<data_el_t>::get_bin_value(long int, long int) const [with data_el_t = int]’:
R_interface.cc:160:27: warning: ‘val’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       return (double) val / count;
                           ^
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:219:19: warning: ‘val’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       val /= count;
                   ^
g++  -I/home/biocbuild/bbs-3.5-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 colorizers.cc:1:0:
colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
    std::auto_ptr<DataVector> data;
         ^
In file included from /usr/include/c++/5/memory:81:0,
                 from colorizers.h:4,
                 from colorizers.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++  -I/home/biocbuild/bbs-3.5-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
display.cc: In function ‘coord hilbert(long long int, int)’:
display.cc:21:46: warning: narrowing conversion of ‘(((long int)c.coord::y) + (1l << (lv + -1)))’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing]
          case 1: { return (coord) { c.x, c.y + ( 1l << (lv-1) ) }; }
                                              ^
display.cc:22:41: warning: narrowing conversion of ‘(((long int)c.coord::x) + (1l << (lv + -1)))’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing]
          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) + (1l << (lv + -1)))’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing]
          case 2: { return (coord) { c.x + ( 1l << (lv-1) ), c.y + ( 1l << (lv-1) ) }; }
                                                                 ^
display.cc:23:50: warning: narrowing conversion of ‘(((1l << lv) + -1l) - ((long int)c.coord::y))’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing]
          case 3: { return (coord) { (1l<<lv) - 1 - c.y, ( 1l << (lv-1) ) - 1 - c.x }; }
                                                  ^
display.cc:23:78: warning: narrowing conversion of ‘(((1l << (lv + -1)) + -1l) - ((long int)c.coord::x))’ from ‘long int’ to ‘int’ inside { } [-Wnarrowing]
          case 3: { return (coord) { (1l<<lv) - 1 - c.y, ( 1l << (lv-1) ) - 1 - c.x }; }
                                                                              ^
g++  -I/home/biocbuild/bbs-3.5-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
g++  -I/home/biocbuild/bbs-3.5-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 window.cc:7:0:
colorizers.h:42:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
    std::auto_ptr<DataVector> data;
         ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /usr/include/glibmm-2.4/glibmm/objectbase.h:32,
                 from /usr/include/glibmm-2.4/glibmm/wrap.h:23,
                 from /usr/include/glibmm-2.4/glibmm/containerhandle_shared.h:26,
                 from /usr/include/glibmm-2.4/glibmm/arrayhandle.h:23,
                 from /usr/include/glibmm-2.4/glibmm.h:91,
                 from /usr/include/gtkmm-2.4/gtkmm.h:87,
                 from window.h:5,
                 from window.cc:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -shared -L/home/biocbuild/bbs-3.5-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 -lfontconfig -lfreetype -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/HilbertVisGUI/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HilbertVisGUI)
BioC 3.5: INSTALL report for HilbertVisGUI on malbec2

Summary

Command output
