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 ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -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/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Motif.cpp -o Motif.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c MotifDistances.cpp -o MotifDistances.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c MotifMatch.cpp -o MotifMatch.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c PlatformSupport.cpp -o PlatformSupport.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c generateScoresDB.cpp -o generateScoresDB.o
g++ -shared -L/usr/local/lib64 -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.Rcheck/MotIV/libs
** 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)