MotIV 1.29.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotIV | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL MotIV
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* installing to library ‘/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-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-3.4-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-3.4-bioc/R/include/Rdefines.h: In member function ‘int PlatformSupport::ReadTransfacFile(SEXP, SEXP)’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:118:31: 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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘filter’ in package ‘MotIV’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘MotIV’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MotIV)