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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MotIV
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MotIV’ ...
** using staged installation
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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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 SmithWatermanAffine::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:883:2: warning: ‘forScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(forScore>revScore){
^~
Alignment.cpp: In member function ‘virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:491:2: warning: ‘forScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(forScore>revScore){
^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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 behavior [-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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 behavior [-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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:39:0,
from PlatformSupport.h:41,
from PlatformSupport.cpp:33:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h: In member function ‘int PlatformSupport::ReadTransfacFile(SEXP, SEXP)’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1629:29: 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;
^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-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 behavior [-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-MotIV/00new/MotIV/libs
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'MotIV' is deprecated and will be removed from Bioconductor
version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (MotIV)