MotIV 1.39.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MotIV |
| Branch: master |
| Last Commit: 389d980 |
| Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MotIV_1.39.0.tar.gz && 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_1.39.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MotIV_1.39.0.zip && rm MotIV_1.39.0.tar.gz MotIV_1.39.0.zip
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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˜1.9-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:1480:31: 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:1480:31: 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_1.39.0.zip
* DONE (MotIV)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MotIV' successfully unpacked and MD5 sums checked