MotIV 1.7.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotIV | | Last Changed Rev: 54811 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:45:05 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/MotIV.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-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 '1.7.0'
* 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 installed package size ... 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 ... OK
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'MotIV' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/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
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c Motif.cpp -o Motif.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c MotifDistances.cpp -o MotifDistances.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c MotifMatch.cpp -o MotifMatch.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c PlatformSupport.cpp -o PlatformSupport.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -IC:/gsl/include -O2 -Wall -c generateScoresDB.cpp -o generateScoresDB.o
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:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/MotIV.Rcheck/MotIV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "MotIV"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'MotIV.Rnw' using 'latin1'
** testing if installed package can be loaded
* DONE (MotIV)