Multiple platform build/check report for BioC 3.6 - CHECK report for HilbertVisGUI on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings HilbertVisGUI_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/HilbertVisGUI.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.36.0’
* 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 ... 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 ... 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 ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -std=c++11
Non-portable flags in variable 'PKG_CFLAGS':
  -std=c++11
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
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 installed files from ‘inst/doc’ ... OK
* 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-3.6-bioc/meat/HilbertVisGUI.Rcheck/00check.log’
for details.

* 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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/HilbertVisGUI.Rcheck/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)

name	user	system	elapsed
hilbertDisplay	0.128	0.032	1.527

CHECK report for HilbertVisGUI on malbec1

Summary

Command output

Installation output

Tests output

Example timings