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BioC 3.1: INSTALL report for MotIV on moscato2

This page was generated on 2015-10-09 09:28:46 -0700 (Fri, 09 Oct 2015).

Package 625/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotIV 1.24.0
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MotIV
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MotIV
Version: 1.24.0
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/MotIV_1.24.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch MotIV_1.24.0.tar.gz && rm MotIV_1.24.0.tar.gz
StartedAt: 2015-10-08 18:59:33 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 19:00:55 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 82.5 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/MotIV_1.24.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch MotIV_1.24.0.tar.gz && rm MotIV_1.24.0.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'MotIV' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
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]
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 [-Wuninitialized]
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 [-Wuninitialized]
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 [-Wuninitialized]
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wuninitialized]
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 [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ColumnComp.cpp -o ColumnComp.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c DeclareAll.cpp -o DeclareAll.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
PlatformSupport.cpp: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
PlatformSupport.cpp:127:27: warning: 'input' may be used uninitialized in this function [-Wuninitialized]
PlatformSupport.cpp:102:10: warning: 'currMotifs' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/i386/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
g++ -m32 -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 -LC:/GSL/i386/lib -lgsl -lgslcblas -lm -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/MotIV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: sapply
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: sapply

install for x64

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'MotIV' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
Alignment.cpp:184:9: warning: variable 'currOne' set but not used [-Wunused-but-set-variable]
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
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]
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 [-Wuninitialized]
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 [-Wuninitialized]
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 [-Wuninitialized]
Alignment.cpp:319:2: warning: 'forScore' may be used uninitialized in this function [-Wuninitialized]
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 [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c ColumnComp.cpp -o ColumnComp.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c DeclareAll.cpp -o DeclareAll.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
Motif.cpp:149:9: warning: variable 'three_base_c' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function 'SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifDistances.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:51:6: warning: variable 'matchTopX' set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:58:7: warning: variable 'ungapped' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function 'SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MotifMatch.cpp:50:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
MotifMatch.cpp:50:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -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]
PlatformSupport.cpp: In member function 'int PlatformSupport::ReadTransfacFile(SEXP, SEXP)':
PlatformSupport.cpp:127:27: warning: 'input' may be used uninitialized in this function [-Wuninitialized]
PlatformSupport.cpp:141:34: warning: 'currMotifs' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/GSL/x64/include    -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function 'SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
generateScoresDB.cpp:54:10: warning: variable 'colChosen' set but not used [-Wunused-but-set-variable]
generateScoresDB.cpp:54:27: warning: variable 'alignChosen' set but not used [-Wunused-but-set-variable]
g++ -m64 -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 -LC:/GSL/x64/lib -lgsl -lgslcblas -lm -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/MotIV/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: sapply
* DONE (MotIV)