BioC 2.6: CHECK report for MotIV on gewurz

Package: MotIV

Version: 1.1.3

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings MotIV_1.1.3.tar.gz

StartedAt: 2010-10-04 17:47:09 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:49:34 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 145.0 seconds

RetCode: 0

Status: OK

CheckDir: MotIV.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/MotIV.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.1.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MotIV' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

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

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


** libs
  making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'virtual double SmithWatermanAffine::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:789: warning: 'forScore' may be used uninitialized in this function
Alignment.cpp: In member function 'virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:588: warning: 'forScore' may be used uninitialized in this function
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:422: warning: 'forScore' may be used uninitialized in this function
Alignment.cpp: In member function 'virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:240: warning: 'forScore' may be used uninitialized in this function
Alignment.cpp:240: warning: 'revScore' may be used uninitialized in this function
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c ColumnComp.cpp -o ColumnComp.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c DeclareAll.cpp -o DeclareAll.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c Motif.cpp -o Motif.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c MotifMatch.cpp -o MotifMatch.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c PlatformSupport.cpp -o PlatformSupport.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c RandPSSMGen.cpp -o RandPSSMGen.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -IC:/GSL_test64/include        -O2 -Wall  -c generateScoresDB.cpp -o generateScoresDB.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o MotIV.dll tmp.def Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -LC:/GSL_test64/lib -lgsl -lgslcblas -lm -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/MotIV.Rcheck/MotIV/libs/x64
  ... done
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "MotIV"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (MotIV)

name	user	system	elapsed
combine	0.95	0.00	0.96
exportAsRangedData	3.38	0.00	3.38
exportAsTransfacFile	0.7	0.0	0.7
filter-class	0	0	0
filter-methods	0	0	0
filter	0.44	0.02	0.45
generateDBScores	0.22	0.00	0.22
getGademPWM	0.19	0.00	0.19
jaspar	0.32	0.01	0.34
makePWM	0	0	0
matches-class	0	0	0
motifMatch	0.38	0.00	0.38
motifOccurences	0	0	0
motiv-class	0	0	0
motiv-methods	0	0	0
plot	5.55	0.02	5.57
readGademPWMFile	0.19	0.00	0.18
readPWMfile	0.03	0.01	0.05
seqLogo	0	0	0
setFilter	0.45	0.00	0.45
split	0.61	0.00	0.61
tf-class	0	0	0
trimPWMedge	0.19	0.00	0.19
viewAlignment	0.42	0.01	0.43
viewMotifs	0.39	0.02	0.41

Summary

Command output