BioC 2.8: CHECK report for MotIV on gewurz

Package: MotIV

Version: 1.5.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings MotIV_1.5.0.tar.gz

StartedAt: 2011-02-24 20:55:28 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:57:43 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 135.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MotIV.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/MotIV.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-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 '1.5.0'
* 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 ... WARNING
Undocumented data sets:
  gadem
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/MotIV.Rcheck/00check.log'
for details

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

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


** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/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:793:9: 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:592:9: 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:244:9: warning: 'forScore' may be used uninitialized in this function
Alignment.cpp:244:19: warning: 'revScore' may be used uninitialized in this function
Alignment.cpp: In member function 'virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:426:9: warning: 'forScore' may be used uninitialized in this function
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c ColumnComp.cpp -o ColumnComp.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c DeclareAll.cpp -o DeclareAll.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c Motif.cpp -o Motif.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c MotifDistances.cpp -o MotifDistances.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c MotifMatch.cpp -o MotifMatch.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c PlatformSupport.cpp -o PlatformSupport.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/include         -O2 -Wall  -c RandPSSMGen.cpp -o RandPSSMGen.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I/src/include -IC:/Rtools212/GSL64/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 MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lws2_32 -LC:/Rtools212/GSL64/lib -lgsl -lgslcblas -lm -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/MotIV.Rcheck/MotIV/libs/x64
** 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	0.84	0.00	0.84
exportAsRangedData	4.24	0.00	4.24
exportAsTransfacFile	0.42	0.00	0.42
filter-class	0	0	0
filter-methods	0.02	0.00	0.02
filter	0.62	0.00	0.62
generateDBScores	0.05	0.00	0.05
getGademPWM	0.19	0.00	0.18
jaspar	0.32	0.00	0.33
makePWM	0	0	0
matches-class	0	0	0
motifDistance	0.61	0.01	0.63
motifMatch	0.35	0.02	0.36
motifOccurences	2.53	0.00	2.53
motiv-class	0	0	0
motiv-methods	0	0	0
plot	4.55	0.02	4.56
readGademPWMFile	0.18	0.00	0.19
readPWMfile	0.05	0.00	0.05
seqLogo	0	0	0
setFilter	0.39	0.00	0.39
split	0.43	0.00	0.44
tf-class	0	0	0
trimPWMedge	0.21	0.01	0.22
viewAlignment	0.37	0.00	0.37
viewMotifs	0.38	0.00	0.38

Summary

Command output