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BioC 3.3: CHECK report for HilbertVisGUI on moscato2

This page was generated on 2016-10-13 12:48:46 -0700 (Thu, 13 Oct 2016).

Package 549/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HilbertVisGUI 1.30.0
Simon Anders
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/HilbertVisGUI
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ ERROR ] ERROR 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: HilbertVisGUI
Version: 1.30.0
Command: rm -rf HilbertVisGUI.buildbin-libdir HilbertVisGUI.Rcheck && mkdir HilbertVisGUI.buildbin-libdir HilbertVisGUI.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HilbertVisGUI.buildbin-libdir HilbertVisGUI_1.30.0.tar.gz >HilbertVisGUI.Rcheck\00install.out 2>&1 && cp HilbertVisGUI.Rcheck\00install.out HilbertVisGUI-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=HilbertVisGUI.buildbin-libdir --install="check:HilbertVisGUI-install.out" --force-multiarch --no-vignettes --timings HilbertVisGUI_1.30.0.tar.gz
StartedAt: 2016-10-13 05:08:04 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 05:08:52 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 47.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: HilbertVisGUI.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HilbertVisGUI.buildbin-libdir HilbertVisGUI.Rcheck && mkdir HilbertVisGUI.buildbin-libdir HilbertVisGUI.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HilbertVisGUI.buildbin-libdir HilbertVisGUI_1.30.0.tar.gz >HilbertVisGUI.Rcheck\00install.out 2>&1 && cp HilbertVisGUI.Rcheck\00install.out HilbertVisGUI-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=HilbertVisGUI.buildbin-libdir --install="check:HilbertVisGUI-install.out" --force-multiarch --no-vignettes --timings HilbertVisGUI_1.30.0.tar.gz
###
##############################################################################
##############################################################################

HilbertVisGUI.Rcheck/00install.out:


install for i386

* installing *source* package 'HilbertVisGUI' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"  -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_env_prot.c -o R_env_prot.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_interface.cc -o R_interface.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/R.h:75:0,
                 from R_interface.cc:17:
E:/biocbld/BBS-3˜1.3-B/R/include/R_ext/RS.h:52:0: warning: "ERROR" redefined
 #define ERROR   ),error(R_problem_buf);}
 ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/windows.h:71:0,
                 from R_interface.cc:13:
C:/Rtools/mingw_32/i686-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<data_el_t>::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<data_el_t>::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_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c colorizers.cc -o colorizers.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c display.cc -o display.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ruler.cc -o ruler.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -mms-bitfields -Ic:/gtkmm/i386/include/gtkmm-2.4 -Ic:/gtkmm/i386/lib/gtkmm-2.4/include -Ic:/gtkmm/i386/include/atkmm-1.6 -Ic:/gtkmm/i386/include/giomm-2.4 -Ic:/gtkmm/i386/lib/giomm-2.4/include -Ic:/gtkmm/i386/include/pangomm-1.4 -Ic:/gtkmm/i386/lib/pangomm-1.4/include -Ic:/gtkmm/i386/include/gtk-2.0 -Ic:/gtkmm/i386/include/gdkmm-2.4 -Ic:/gtkmm/i386/lib/gdkmm-2.4/include -Ic:/gtkmm/i386/include/atk-1.0 -Ic:/gtkmm/i386/include/glibmm-2.4 -Ic:/gtkmm/i386/lib/glibmm-2.4/include -Ic:/gtkmm/i386/include/glib-2.0 -Ic:/gtkmm/i386/lib/glib-2.0/include -Ic:/gtkmm/i386/include/sigc++-2.0 -Ic:/gtkmm/i386/lib/sigc++-2.0/include -Ic:/gtkmm/i386/include/cairomm-1.0 -Ic:/gtkmm/i386/lib/cairomm-1.0/include -Ic:/gtkmm/i386/include/pango-1.0 -Ic:/gtkmm/i386/include/cairo -Ic:/gtkmm/i386/include -Ic:/gtkmm/i386/include/freetype2 -Ic:/gtkmm/i386/include/libpng14 -Ic:/gtkmm/i386/lib/gtk-2.0/include -Ic:/gtkmm/i386/include/gdk-pixbuf-2.0   -DSO_NAME=HilbertVisGUI -DMSWINDOWS    -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c window.cc -o window.o
C:/Rtools/mingw_32/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:/gtkmm/i386/lib -Lc:/devel/dist/win32/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:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/HilbertVisGUI.buildbin-libdir/HilbertVisGUI/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct NULL not valid
ERROR: loading failed
* removing 'E:/biocbld/bbs-3.3-bioc/meat/HilbertVisGUI.buildbin-libdir/HilbertVisGUI'
Warning: running command 'E:/biocbld/bbs-3.3-bioc/R/bin/i386/Rcmd.exe INSTALL --library=HilbertVisGUI.buildbin-libdir HilbertVisGUI_1.30.0.tar.gz --no-multiarch' had status 1