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BUILD BIN report for MotIV on tokay2

This page was generated on 2019-10-16 12:23:34 -0400 (Wed, 16 Oct 2019).

Package 1045/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotIV 1.40.0
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MotIV
Branch: RELEASE_3_9
Last Commit: 3ab399d
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MotIV
Version: 1.40.0
Command: rm -rf MotIV.buildbin-libdir && mkdir MotIV.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MotIV.buildbin-libdir MotIV_1.40.0.tar.gz
StartedAt: 2019-10-16 09:43:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:44:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 52.0 seconds
RetCode: 0
Status:  OK  
PackageFile: MotIV_1.40.0.zip
PackageFileSize: 1.91 MiB

Command output

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###
### Running command:
###
###   rm -rf MotIV.buildbin-libdir && mkdir MotIV.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MotIV.buildbin-libdir MotIV_1.40.0.tar.gz
###
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install for i386

* installing *source* package 'MotIV' ...
** using staged installation

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ColumnComp.cpp -o ColumnComp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c DeclareAll.cpp -o DeclareAll.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rinternals.h:1481:31: 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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RandPSSMGen.cpp -o RandPSSMGen.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MotIV.buildbin-libdir/00LOCK-MotIV/00new/MotIV/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'filter' in package 'MotIV'
** help
*** installing help indices
  converting help for package 'MotIV'
    finding HTML links ... done
    FOXA_rGADEM                             html  
    aligns-class                            html  
    as.data.frame                           html  
    combineMotifs                           html  
    exportAsRangedData                      html  
    exportAsTransfacFile                    html  
    filter-class                            html  
    filter-methods                          html  
    filter                                  html  
    generateDBScores                        html  
    getGademPWM                             html  
    getPWM                                  html  
    jaspar                                  html  
    makePWM                                 html  
    matches-class                           html  
    motifDistance                           html  
    motifMatch                              html  
    motifOccurences                         html  
    motiv-class                             html  
    motiv-methods                           html  
    plot                                    html  
    readGademPWMFile                        html  
    readPWMfile                             html  
    seqLogo2                                html  
    setFilter                               html  
    split                                   html  
    tf-class                                html  
    trimPWMedge                             html  
    viewAlignment                           html  
    viewMotifs                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ColumnComp.cpp -o ColumnComp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c DeclareAll.cpp -o DeclareAll.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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-3~1.9-B/R/include/Rinternals.h: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/Rinternals.h:1481:31: 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-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RandPSSMGen.cpp -o RandPSSMGen.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MotIV' as MotIV_1.40.0.zip
* DONE (MotIV)