BioC 3.5: INSTALL report for MotIV on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL MotIV
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘MotIV’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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: ‘revScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if(forScore>revScore){
  ^
Alignment.cpp:319:2: warning: ‘forScore’ 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){
  ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ColumnComp.cpp -o ColumnComp.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DeclareAll.cpp -o DeclareAll.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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];
         ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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; 
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
                           ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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:41:0,
                 from PlatformSupport.h:41,
                 from PlatformSupport.cpp:33:
/home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h: In member function ‘int PlatformSupport::ReadTransfacFile(SEXP, SEXP)’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:122:31: warning: ‘input’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NUMERIC_DATA(x)  (REAL(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; 
          ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
                           ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/MotIV/libs
** 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
* DONE (MotIV)
BioC 3.5: INSTALL report for MotIV on malbec2

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