BioC 2.14: CHECK report for ternarynet on zin2

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ternarynet_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ternarynet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ternarynet’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/ternarynet.Rcheck/00check.log’
for details.

* installing *source* package ‘ternarynet’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tnetfit.cc -o tnetfit.o
tnetfit.cc: In function ‘SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetfit.cc:24:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
tnetfit.cc:24:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
tnetfit.cc:24:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
tnetfit.cc:311:53: warning: ‘newScore’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:207:42: warning: ‘muci_old’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:202:44: warning: ‘sigmaci’ may be used uninitialized in this function [-Wuninitialized]
tnetfit.cc:207:42: warning: ‘sigma0’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.14-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:469:5: warning: unused variable ‘tableWidth’ [-Wunused-variable]
tnetfuncs.cc:477:5: warning: unused variable ‘ipause’ [-Wunused-variable]
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:567:6: warning: unused variable ‘ipause’ [-Wunused-variable]
tnetfuncs.cc:571:16: warning: unused variable ‘i’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tnetpost.cc -o tnetpost.o
tnetpost.cc: In function ‘SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetpost.cc:25:9: warning: unused variable ‘ipause’ [-Wunused-variable]
tnetpost.cc:27:9: warning: unused variable ‘m0fit’ [-Wunused-variable]
tnetpost.cc:28:32: warning: variable ‘minScore’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:28:42: warning: unused variable ‘finalScore’ [-Wunused-variable]
tnetpost.cc:30:9: warning: unused variable ‘l0’ [-Wunused-variable]
tnetpost.cc:30:13: warning: unused variable ‘stage_count’ [-Wunused-variable]
tnetpost.cc:30:26: warning: unused variable ‘tempi’ [-Wunused-variable]
tnetpost.cc:30:33: warning: unused variable ‘jtrans’ [-Wunused-variable]
tnetpost.cc:30:41: warning: unused variable ‘nTransition’ [-Wunused-variable]
tnetpost.cc:36:21: warning: variable ‘xSeedFit’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:38:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:39:9: warning: variable ‘maxStage’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:39:19: warning: variable ‘maxTransition’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:12: warning: variable ‘epsilon’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:21: warning: variable ‘chi0’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:27: warning: variable ‘delta’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:40:34: warning: variable ‘rho’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:41:9: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:44:9: warning: variable ‘ne’ set but not used [-Wunused-but-set-variable]
tnetpost.cc:150:10: warning: variable ‘minDump’ set but not used [-Wunused-but-set-variable]
g++ -shared -L/usr/local/lib -o ternarynet.so tnetfit.o tnetfuncs.o tnetpost.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/ternarynet.Rcheck/ternarynet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ternarynet)

name	user	system	elapsed
attractorSummary	3.928	0.000	3.930
graphPosterior	3.936	0.000	3.949
plotFit	3.880	0.000	3.885
plotPost	3.945	0.004	3.953
plotTraces	4.008	0.000	4.015
predictAttractor	4.08	0.00	4.09
simulateSteadyState	0.000	0.004	0.004
ternaryFit-class	4.004	0.000	4.012
ternaryFitParameters-class	0.004	0.000	0.003
ternaryPost-class	4.025	0.000	4.030
tnetfit	4.188	0.004	4.214
tnetpost	3.976	0.000	3.983

BioC 2.14: CHECK report for ternarynet on zin2

Summary

Command output