Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for MotIV on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:05 -0400 (Tue, 27 Oct 2015).

Package 672/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotIV 1.26.0
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MotIV
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MotIV
Version: 1.26.0
Command: rm -rf MotIV.buildbin-libdir MotIV.Rcheck && mkdir MotIV.buildbin-libdir MotIV.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MotIV.buildbin-libdir MotIV_1.26.0.tar.gz >MotIV.Rcheck\00install.out 2>&1 && cp MotIV.Rcheck\00install.out MotIV-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MotIV.buildbin-libdir --install="check:MotIV-install.out" --force-multiarch --no-vignettes --timings MotIV_1.26.0.tar.gz
StartedAt: 2015-10-27 03:49:01 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:53:47 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 285.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MotIV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MotIV.buildbin-libdir MotIV.Rcheck && mkdir MotIV.buildbin-libdir MotIV.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MotIV.buildbin-libdir MotIV_1.26.0.tar.gz >MotIV.Rcheck\00install.out 2>&1 && cp MotIV.Rcheck\00install.out MotIV-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MotIV.buildbin-libdir --install="check:MotIV-install.out" --force-multiarch --no-vignettes --timings MotIV_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MotIV.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MotIV' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motifDistances: no visible binding for global variable 'jaspar.scores'
motifMatch: no visible binding for global variable 'jaspar'
motifMatch: no visible binding for global variable 'jaspar.scores'
[,motiv-ANY-ANY : .local: no visible binding for global variable 'ANY'
plot,motiv-ANY: no visible binding for global variable 'y'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/biocbld/bbs-3.2-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/i386/MotIV.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'C:/biocbld/bbs-3.2-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/x64/MotIV.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [25s] OK
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
exportAsRangedData 5.48   0.01    8.28
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/MotIV.Rcheck/00check.log'
for details.

MotIV.Rcheck/00install.out:


install for i386

* installing *source* package 'MotIV' ...

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


** libs
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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 -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/i386
** 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

install for x64

* installing *source* package 'MotIV' ...

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


** libs
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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"C:/biocbld/BBS-3˜1.2-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 -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/MotIV.buildbin-libdir/MotIV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MotIV' as MotIV_1.26.0.zip
* DONE (MotIV)

MotIV.Rcheck/examples_i386/MotIV-Ex.timings:

nameusersystemelapsed
FOXA_rGADEM0.780.010.80
as.data.frame0.520.060.58
combineMotifs0.500.020.51
exportAsRangedData4.150.054.89
exportAsTransfacFile0.530.000.53
filter-class000
filter-methods000
filter0.520.010.53
generateDBScores0.030.000.04
getGademPWM0.270.000.26
jaspar0.390.030.42
makePWM000
matches-class000
motifDistance0.530.000.55
motifMatch0.760.000.80
motifOccurences1.550.021.56
motiv-class000
motiv-methods000
plot2.840.002.84
readGademPWMFile0.210.010.22
readPWMfile0.030.000.03
seqLogo2000
setFilter0.290.000.30
split0.320.000.31
tf-class000
trimPWMedge0.170.000.17
viewAlignment0.300.040.33
viewMotifs0.280.010.30

MotIV.Rcheck/examples_x64/MotIV-Ex.timings:

nameusersystemelapsed
FOXA_rGADEM0.560.021.55
as.data.frame0.960.011.77
combineMotifs0.550.020.95
exportAsRangedData5.480.018.28
exportAsTransfacFile0.520.000.92
filter-class000
filter-methods000
filter0.590.000.60
generateDBScores0.040.000.03
getGademPWM0.280.000.28
jaspar0.510.030.55
makePWM000
matches-class000
motifDistance0.420.000.92
motifMatch0.390.000.39
motifOccurences1.390.021.41
motiv-class0.020.000.02
motiv-methods000
plot2.340.032.37
readGademPWMFile0.140.020.15
readPWMfile0.010.000.02
seqLogo2000
setFilter0.300.010.31
split0.340.020.36
tf-class000
trimPWMedge0.140.000.14
viewAlignment0.310.000.31
viewMotifs0.350.000.34