MotIV 1.5.0
Eloi Mercier , Raphael Gottardo
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotIV | | Last Changed Rev: 50295 / Revision: 53255 | | Last Changed Date: 2010-10-17 22:57:44 -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 |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/MotIV.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 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 ... 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
'/Users/biocbuild/bbs-2.8-bioc/meat/MotIV.Rcheck/00check.log'
for details
* installing *source* package 'MotIV' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
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 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function 'virtual double SmithWatermanAffine::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)':
Alignment.cpp:793: 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: 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:426: 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: warning: 'revScore' may be used uninitialized in this function
Alignment.cpp:244: warning: 'forScore' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ColumnComp.cpp -o ColumnComp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c DeclareAll.cpp -o DeclareAll.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Motif.cpp -o Motif.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c MotifDistances.cpp -o MotifDistances.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c MotifMatch.cpp -o MotifMatch.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c PlatformSupport.cpp -o PlatformSupport.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c generateScoresDB.cpp -o generateScoresDB.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-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 ...
** testing if installed package can be loaded
* DONE (MotIV)