BioC 2.10: CHECK report for ternarynet on petty

Package: ternarynet

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ternarynet_1.0.0.tar.gz

StartedAt: 2012-09-24 01:54:42 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:56:22 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 100.4 seconds

RetCode: 0

Status: OK

CheckDir: ternarynet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/ternarynet.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ternarynet/DESCRIPTION' ... OK
* this is package 'ternarynet' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'ternarynet' 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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 'ternarynet' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c tnetfit.cc -o tnetfit.o
tnetfit.cc: In function 'SEXPREC* tnetfit(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
tnetfit.cc:73: warning: unused variable 'tempi'
tnetfit.cc:98: warning: 'muci_old' may be used uninitialized in this function
tnetfit.cc:98: warning: 'sigmaci' may be used uninitialized in this function
tnetfit.cc:98: warning: 'sigma0' may be used uninitialized in this function
tnetfit.cc:77: warning: 'newScore' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc: In function 'double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)':
tnetfuncs.cc:427: warning: unused variable 'tableWidth'
tnetfuncs.cc:435: warning: unused variable 'ipause'
tnetfuncs.cc: In function 'double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)':
tnetfuncs.cc:517: warning: unused variable 'ipause'
tnetfuncs.cc:521: warning: unused variable 'i'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c tnetpost.cc -o tnetpost.o
tnetpost.cc: In function 'SEXPREC* tnetpost(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
tnetpost.cc:25: warning: unused variable 'ipause'
tnetpost.cc:27: warning: unused variable 'm0fit'
tnetpost.cc:28: warning: unused variable 'finalScore'
tnetpost.cc:30: warning: unused variable 'l0'
tnetpost.cc:30: warning: unused variable 'stage_count'
tnetpost.cc:30: warning: unused variable 'tempi'
tnetpost.cc:30: warning: unused variable 'jtrans'
tnetpost.cc:30: warning: unused variable 'nTransition'
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/ternarynet.Rcheck/ternarynet/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ternarynet.Rnw' 
** testing if installed package can be loaded

* DONE (ternarynet)

name	user	system	elapsed
attractorSummary	8.052	0.003	8.056
graphPosterior	7.937	0.002	7.940
plotTraces	8.013	0.003	8.016
ternaryFit-class	9.890	0.003	9.893
ternaryFitParameters-class	0.003	0.000	0.004
ternaryPost-class	11.828	0.005	11.833
tnetfit	9.902	0.003	9.906
tnetpost	8.577	0.003	8.581

Summary

Command output