Package: ternarynet

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ternarynet_1.22.0.tar.gz

StartedAt: 2018-04-12 10:16:20 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:17:51 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 91.2 seconds

RetCode: 0

Status:  OK

CheckDir: ternarynet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ternarynet_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ternarynet.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.22.0’
* 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 ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ternarynet’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotFit: no visible global function definition for ‘plot’
plotPost: no visible global function definition for ‘plot’
plotTraces: no visible global function definition for ‘par’
plotTraces: no visible global function definition for ‘plot’
ternaryFit: no visible global function definition for ‘new’
ternaryFitParameters: no visible global function definition for ‘new’
ternaryPost: no visible global function definition for ‘new’
tnetfit: no visible global function definition for ‘runif’
tnetpost: no visible global function definition for ‘runif’
backupStage<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
beta0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
chi0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
degreeObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
degreeObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
delta<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
edgePenalty<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
epsilon<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
experimentNames<-,ternaryFit: no visible global function definition for
  ‘validObject’
experimentNames<-,ternaryPost: no visible global function definition
  for ‘validObject’
finalTemperature<-,ternaryFit: no visible global function definition
  for ‘validObject’
geneNames<-,ternaryFit: no visible global function definition for
  ‘validObject’
geneNames<-,ternaryPost: no visible global function definition for
  ‘validObject’
graphObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
graphObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
inputParams<-,ternaryFit: no visible global function definition for
  ‘validObject’
inputParams<-,ternaryPost: no visible global function definition for
  ‘validObject’
m0<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
maxDegree<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
maxStage<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
maxTransition<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
minScore<-,ternaryFit: no visible global function definition for
  ‘validObject’
ne<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
neighborDegree<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
newScore<-,ternaryFit: no visible global function definition for
  ‘validObject’
pAddParent<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
pExchangeParent<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
pNeighborhood<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
perturbationObj<-,ternaryFit: no visible global function definition for
  ‘validObject’
perturbationObj<-,ternaryPost: no visible global function definition
  for ‘validObject’
perturbationType<-,ternaryFitParameters: no visible global function
  definition for ‘validObject’
rho<-,ternaryFitParameters: no visible global function definition for
  ‘validObject’
scoreType<-,ternaryFitParameters: no visible global function definition
  for ‘validObject’
scores<-,ternaryPost: no visible global function definition for
  ‘validObject’
stageCount<-,ternaryFit: no visible global function definition for
  ‘validObject’
steadyStateObj<-,ternaryFit: no visible global function definition for
  ‘validObject’
steadyStateObj<-,ternaryPost: no visible global function definition for
  ‘validObject’
tableObjMin<-,ternaryFit: no visible global function definition for
  ‘validObject’
tableObjs<-,ternaryPost: no visible global function definition for
  ‘validObject’
traces<-,ternaryFit: no visible global function definition for
  ‘validObject’
xSeed<-,ternaryFit: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  new par plot runif validObject
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotPost          6.165  0.012   6.280
attractorSummary  5.837  0.016   5.975
graphPosterior    5.700  0.009   5.782
plotFit           5.559  0.010   5.663
ternaryPost-class 5.070  0.009   5.144
ternaryFit-class  4.950  0.009   5.040
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ternarynet.Rcheck/00check.log’
for details.

* installing *source* package ‘ternarynet’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnetfit.cc -o tnetfit.o
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
    int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
                                      ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
    ^
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
    ^
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
        int m1, m2, i;
                    ^
tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable]
        int ipause; 
            ^
4 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnetpost.cc -o tnetpost.o
tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                         ^
tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
            ^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
        ^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                        ^
tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable]
    int l0, stage_count, tempi, jtrans, nTransition;
                                ^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
    int m0fit;
        ^
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
    int ipause;
        ^
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
    double newScore, oldScore, minScore, finalScore;
                                         ^
8 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -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-3.6-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	5.837	0.016	5.975
graphPosterior	5.700	0.009	5.782
plotFit	5.559	0.010	5.663
plotPost	6.165	0.012	6.280
plotTraces	4.807	0.010	4.878
predictAttractor	4.485	0.010	4.583
simulateSteadyState	0.013	0.000	0.013
ternaryFit-class	4.950	0.009	5.040
ternaryFitParameters-class	0.002	0.000	0.003
ternaryPost-class	5.070	0.009	5.144
tnetfit	4.847	0.009	4.902
tnetpost	4.733	0.008	4.811