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Package 267/419HostnameOS / ArchBUILDCHECKBUILD BIN
MotIV 1.4.0
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/MotIV
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: MotIV
Version: 1.4.0
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings MotIV_1.4.0.tar.gz
StartedAt: 2011-03-31 09:26:32 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 09:29:43 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 190.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MotIV.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/MotIV.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.4.0'
* 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) and $(LAPACK_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-2.7-bioc/meat/MotIV.Rcheck/00check.log'
for details

MotIV.Rcheck/00install.out:

* 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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-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˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-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)

MotIV.Rcheck/MotIV-Ex.timings:

nameusersystemelapsed
combine0.820.010.85
exportAsRangedData4.680.004.67
exportAsTransfacFile0.420.000.42
filter-class000
filter-methods000
filter0.400.000.41
generateDBScores0.050.000.04
getGademPWM0.190.000.19
jaspar0.340.020.36
makePWM000
matches-class0.020.000.02
motifDistance0.370.000.37
motifMatch0.390.000.39
motifOccurences2.570.002.56
motiv-class000
motiv-methods000
plot4.310.004.31
readGademPWMFile0.190.000.19
readPWMfile0.060.000.06
seqLogo000
setFilter0.390.000.39
split0.400.000.39
tf-class000
trimPWMedge0.180.000.19
viewAlignment0.410.000.41
viewMotifs0.370.000.37