BioC 3.5: CHECK report for MotIV on tokay2

Package: MotIV

Version: 1.32.0

Command: rm -rf MotIV.buildbin-libdir MotIV.Rcheck && mkdir MotIV.buildbin-libdir MotIV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MotIV.buildbin-libdir MotIV_1.32.0.tar.gz >MotIV.Rcheck\00install.out 2>&1 && cp MotIV.Rcheck\00install.out MotIV-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MotIV.buildbin-libdir --install="check:MotIV-install.out" --force-multiarch --no-vignettes --timings MotIV_1.32.0.tar.gz

StartedAt: 2017-08-16 01:24:58 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:30:31 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 332.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MotIV.Rcheck

Warnings: 1

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###
### Running command:
###
###   rm -rf MotIV.buildbin-libdir MotIV.Rcheck && mkdir MotIV.buildbin-libdir MotIV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MotIV.buildbin-libdir MotIV_1.32.0.tar.gz >MotIV.Rcheck\00install.out 2>&1 && cp MotIV.Rcheck\00install.out MotIV-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MotIV.buildbin-libdir --install="check:MotIV-install.out" --force-multiarch --no-vignettes --timings MotIV_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.32.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MotIV' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
motifDistances: no visible binding for global variable 'jaspar.scores'
motifDistances: no visible global function definition for 'as.dist'
motifMatch: no visible binding for global variable 'jaspar'
motifMatch: no visible binding for global variable 'jaspar.scores'
plotDistanceHistogram: no visible global function definition for 'hist'
plotDistributionHistogram: no visible global function definition for
  'hist'
[,motiv-ANY-ANY-ANY: no visible binding for global variable 'ANY'
Undefined global functions or variables:
  ANY as.dist hist jaspar jaspar.scores
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'motiv,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/i386/MotIV.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
exportAsRangedData 6.56   0.04    6.61
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MotIV' ...

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


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'double Alignment::AlignMotifs2D(Motif*, Motif*, int&, int&, int&, bool&, bool&)':
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
  double score1, score2, bestScore=0;
                 ^
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                  ^
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                        ^
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
  int aL_A, aL_B; 
            ^
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
  bool for_A, for_B;
              ^
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
  Motif* currOne = one;
         ^
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
  Motif* currTwo = two;
         ^
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:423:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  double tmp;
         ^
Alignment.cpp: In member function 'virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
Alignment.cpp:319:2: warning: 'revScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
Alignment.cpp: In member function 'virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:713:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ColumnComp.cpp -o ColumnComp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c DeclareAll.cpp -o DeclareAll.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Motif.cpp -o Motif.o
Motif.cpp: In member function 'char Motif::ColConsensus(int)':
Motif.cpp:148:7: warning: variable 'three_base_l' set but not used [-Wunused-but-set-variable]
  char three_base_l[4]; //three base consensus
       ^
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
  double three_base_c[4];
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:115:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
  int matchTopX = TOP_MATCH;
      ^
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
  bool ungapped=false; 
       ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:120:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp: In member function 'void PlatformSupport::PreAlign(Alignment*)':
PlatformSupport.cpp:412:47: warning: variable 'max_score' set but not used [-Wunused-but-set-variable]
  double curr_score, curr_z_score, curr_p_val, max_score;
                                               ^
In file included from Motif.h:39:0,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rinternals.h:1291:31: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define length(x)  Rf_length(x)
                               ^
PlatformSupport.cpp:103:18: note: 'input' was declared here
  SEXP inputName, input;
                  ^
PlatformSupport.cpp:102:10: warning: 'currMotifs' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Motif** currMotifs; int currCnt; 
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RandPSSMGen.cpp -o RandPSSMGen.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:127:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MotIV.dll tmp.def Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'MotIV'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MotIV' ...

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


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'double Alignment::AlignMotifs2D(Motif*, Motif*, int&, int&, int&, bool&, bool&)':
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
  double score1, score2, bestScore=0;
                 ^
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                  ^
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
  int i1_A, i2_A, i1_B, i2_B;
                        ^
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
  int aL_A, aL_B; 
            ^
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
  bool for_A, for_B;
              ^
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
  Motif* currOne = one;
         ^
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
  Motif* currTwo = two;
         ^
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:423:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  double tmp;
         ^
Alignment.cpp: In member function 'virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
Alignment.cpp:319:2: warning: 'revScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
Alignment.cpp: In member function 'virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:713:2: warning: 'forScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ColumnComp.cpp -o ColumnComp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c DeclareAll.cpp -o DeclareAll.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Motif.cpp -o Motif.o
Motif.cpp: In member function 'char Motif::ColConsensus(int)':
Motif.cpp:148:7: warning: variable 'three_base_l' set but not used [-Wunused-but-set-variable]
  char three_base_l[4]; //three base consensus
       ^
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
  double three_base_c[4];
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:115:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
  int matchTopX = TOP_MATCH;
      ^
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
  bool ungapped=false; 
       ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:120:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp: In member function 'void PlatformSupport::PreAlign(Alignment*)':
PlatformSupport.cpp:412:47: warning: variable 'max_score' set but not used [-Wunused-but-set-variable]
  double curr_score, curr_z_score, curr_p_val, max_score;
                                               ^
In file included from Motif.h:39:0,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rinternals.h:1291:31: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define length(x)  Rf_length(x)
                               ^
PlatformSupport.cpp:103:18: note: 'input' was declared here
  SEXP inputName, input;
                  ^
PlatformSupport.cpp:102:10: warning: 'currMotifs' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Motif** currMotifs; int currCnt; 
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RandPSSMGen.cpp -o RandPSSMGen.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:127:11: warning: deleting object of abstract class type 'ColumnComp' which has non-virtual destructor will cause undefined behaviour [-Wdelete-non-virtual-dtor]
  delete(CC);
           ^
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
          ^
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
     bool colChosen=false, alignChosen=false;
                           ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MotIV.dll tmp.def Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MotIV' as MotIV_1.32.0.zip
* DONE (MotIV)

name	user	system	elapsed
FOXA_rGADEM	0.40	0.02	0.41
as.data.frame	0.67	0.00	0.67
combineMotifs	0.36	0.02	0.37
exportAsRangedData	3.25	0.01	3.27
exportAsTransfacFile	0.43	0.03	0.47
filter-class	0	0	0
filter-methods	0	0	0
filter	0.35	0.02	0.36
generateDBScores	0.03	0.00	0.03
getGademPWM	0.2	0.0	0.2
jaspar	0.31	0.01	0.33
makePWM	0	0	0
matches-class	0	0	0
motifDistance	0.43	0.05	0.48
motifMatch	0.40	0.00	0.41
motifOccurences	1.74	0.03	1.76
motiv-class	0	0	0
motiv-methods	0	0	0
plot	3.03	0.02	3.05
readGademPWMFile	0.21	0.00	0.20
readPWMfile	0.01	0.00	0.02
seqLogo2	0	0	0
setFilter	0.36	0.00	0.36
split	0.33	0.00	0.32
tf-class	0	0	0
trimPWMedge	0.19	0.01	0.21
viewAlignment	0.39	0.10	0.48
viewMotifs	0.50	0.01	0.51

name	user	system	elapsed
FOXA_rGADEM	0.61	0.05	0.66
as.data.frame	0.64	0.03	0.67
combineMotifs	0.66	0.00	0.65
exportAsRangedData	6.56	0.04	6.61
exportAsTransfacFile	0.36	0.00	0.36
filter-class	0	0	0
filter-methods	0	0	0
filter	0.31	0.00	0.31
generateDBScores	0.03	0.00	0.03
getGademPWM	0.31	0.00	0.32
jaspar	0.50	0.04	0.53
makePWM	0	0	0
matches-class	0	0	0
motifDistance	0.35	0.01	0.36
motifMatch	0.39	0.00	0.39
motifOccurences	1.29	0.03	1.32
motiv-class	0	0	0
motiv-methods	0	0	0
plot	3.22	0.00	3.22
readGademPWMFile	0.16	0.00	0.16
readPWMfile	0.03	0.00	0.03
seqLogo2	0	0	0
setFilter	0.31	0.02	0.33
split	0.3	0.0	0.3
tf-class	0	0	0
trimPWMedge	0.29	0.00	0.28
viewAlignment	0.48	0.01	0.50
viewMotifs	0.33	0.02	0.35