BioC 2.10: CHECK report for ternarynet on lamb2

Package: ternarynet

Version: 1.0.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.0.0.tar.gz

StartedAt: 2012-09-24 04:01:36 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 04:02:19 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 43.4 seconds

RetCode: 0

Status: OK

CheckDir: ternarynet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ternarynet.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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:73:39: warning: unused variable ‘tempi’
tnetfit.cc:77:12: warning: ‘newScore’ may be used uninitialized in this function
tnetfit.cc:98:12: warning: ‘sigma0’ may be used uninitialized in this function
tnetfit.cc:98:20: warning: ‘sigmaci’ may be used uninitialized in this function
tnetfit.cc:98:45: warning: ‘muci_old’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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:427:5: warning: unused variable ‘tableWidth’
tnetfuncs.cc:435:5: 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:517:6: warning: unused variable ‘ipause’
tnetfuncs.cc:521:16: warning: unused variable ‘i’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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:25:9: warning: unused variable ‘ipause’
tnetpost.cc:27:9: warning: unused variable ‘m0fit’
tnetpost.cc:28:42: warning: unused variable ‘finalScore’
tnetpost.cc:30:9: warning: unused variable ‘l0’
tnetpost.cc:30:13: warning: unused variable ‘stage_count’
tnetpost.cc:30:26: warning: unused variable ‘tempi’
tnetpost.cc:30:33: warning: unused variable ‘jtrans’
tnetpost.cc:30:41: warning: unused variable ‘nTransition’
g++ -shared -L/usr/local/lib64 -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/ternarynet.Rcheck/ternarynet/libs
** 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	2.896	0.004	2.917
graphPosterior	2.872	0.004	2.890
plotTraces	2.864	0.000	2.862
ternaryFit-class	2.856	0.000	2.855
ternaryFitParameters-class	0.004	0.000	0.003
ternaryPost-class	2.840	0.000	2.843
tnetfit	2.857	0.000	2.858
tnetpost	2.860	0.000	2.862

Summary

Command output